Ethanol production from lignocellulosic hydrolysates using engineered Saccharomyces cerevisiae harboring xylose isomerase-based pathway

Xylose isomerase: From fundamental research to applied enzyme technology

Xylose isomerases (XI, EC 5.3.1.5) are key enzymes for the metabolism of pentoses by microorganisms. The importance of XIs goes beyond academic biochemical research and the catalysis of aldo-ketose conversion by XIs is among the most successful examples of industrial enzyme technology in a market that generates multibillion dollar annual revenues. Here we present an in-depth review of how structural information has contributed to the current understanding of XI catalysis, and discuss topics related to the ongoing efforts to elucidate key aspects of the catalytic mechanism. An overview of XI immobilization is also provided that illustrates how the discoveries in basic enzyme technology research can generate opportunities for novel uses of XI, and we review not only historical aspects but also more recent applications in HFCS, biofuels and other applications. The systems biology revolution will impact all aspects of XI research and application, and we finalize by reviewing the contemporary efforts of metabolic and protein engineering using XI and the future roles of the enzyme in the expanding bioeconomy.

Enhanced physicochemical characteristics and biological activities of low-temperature ethylenediamine/urea pretreated lignin

Low-temperature ethylenediamine (EDA)/urea pretreatment had been demonstrated to be an efficient pretreatment method for enzymatic hydrolysis and bioethanol production. For high-value utilization of the third main components of lignocellulosic biomass, the physicochemical structure characteristics and biological activities of low-temperature EDA/urea pretreated lignin (EUL) were comprehensively investigated in the present study. The results demonstrated that the pretreatment process facilitated the depolymerization of lignin, resulting in notable reduction in molecular weight and polydispersity index from 2.32 to 1.42 kg/mol and 1.44 to 1.20, respectively. The EDA/urea pretreated lignin (EUL) exhibited enhanced ultraviolet absorption capacity and the most significant DPPH radical scavenging and inhibition of Staphylococcus aureus in comparison to the primary lignin (PL) and the NaOH pretreated lignin (NL). Enhanced physicochemical characteristics and biological activities of EUL make it more suitable to be developed as sunscreen ingredient or antioxidant and antimicrobial agent in food preservation and conservation.

Synthetic biology approaches to improve tolerance of inhibitors in lignocellulosic hydrolysates

Increasing attention is being focused on using lignocellulose for valuable products. Microbial decomposition can convert lignocellulose into renewable biofuels and other high-value bioproducts, contributing to sustainable development. However, the presence of inhibitors in lignocellulosic hydrolysates can negatively affect microorganisms during fermentation. Improving microbial tolerance to these hydrolysates is a major focus in metabolic engineering. Traditional detoxification methods increase costs, so there is a need for cheap and efficient cell-based detoxification strategies. Synthetic biology approaches offer several strategies for improving microbial tolerance, including redox balancing, membrane engineering, omics-guided technologies, expression of protectants and transcription factors, irrational engineering, cell flocculation, and other novel technologies. Advances in molecular biology, high-throughput sequencing, and artificial intelligence (AI) allow for precise strain modification and efficient industrial production. Developing AI-based computational models to guide synthetic biology efforts and creating large-scale heterologous libraries with automation and high-throughput technologies will be important for future research.

Efficient calcium fumarate overproduction from xylose and corncob-derived xylose by engineered strains of Aureobasidium pullulans var. Aubasidani DH177

BACKGROUND

Xylose from lignocellulose is one of the most abundant and important renewable and green raw materials. It is very important how to efficiently transform xylose into useful bioproducts such as fumaric acid and so on.

RESULTS

In this study, it was found that the GC1 strain (∆gox, in which the GOX gene encoding glucose oxidase which could transform glucose into gluconic acid was removed) of A. pullulans var. aubasidani DH177 had the high ability to utilize xylose and corncob-derived xylose with CO2 fixation derived from CaCO3 to produce calcium fumarate. Overexpression of the XI gene encoding xylose isomerase, the XK gene encoding xylose kinase and the TKL gene coding for transketolase made the strain TKL-4 produce 73.1 g/L of calcium fumarate from xylose. At the same time, the transcriptional levels of the key ASS gene coding for argininosuccinate synthase and the ASL gene coding for argininosuccinate lyase in the ornithine-urea cycle (OUC) were also obviously enhanced. The results also demonstrated that the TKL-4 strain could produce more calcium fumarate from xylose and corncob-derived xylose than from glucose. During 10-liter fermentation, the TKL-4 strain could produce 88.5 g/L of calcium fumarate from xylose, the productivity was 0.52 g/h/L. Meanwhile, it could yield 85.6 g/L of calcium fumarate from corncob-derived xylose and the productivity was 0.51 g/h/L. During the same fermentation, the TKL-4 strain could transform the mixture containing 75.0 g/L glucose and 45.0 g/L xylose to produce 78.7 ± 1.1 g/L calcium fumarate.

CONCLUSIONS

This indicated that the TKL-4 strain constructed in this study indeed could actively transform xylose and corncob-derived xylose into calcium fumarate through the green ways.

Saccharomyces cerevisiae for lignocellulosic ethanol production: a look at key attributes and genome shuffling

These days, bioethanol research is looking at using non-edible plant materials, called lignocellulosic feedstocks, because they are cheap, plentiful, and renewable. However, these materials are complex and require pretreatment to release fermentable sugars. Saccharomyces cerevisiae, the industrial workhorse for bioethanol production, thrives in sugary environments and can handle high levels of ethanol. However, during lignocellulose fermentation, S. cerevisiae faces challenges like high sugar and ethanol concentrations, elevated temperatures, and even some toxic substances present in the pretreated feedstocks. Also, S. cerevisiae struggles to efficiently convert all the sugars (hexose and pentose) present in lignocellulosic hydrolysates. That's why scientists are exploring the natural variations within Saccharomyces strains and even figuring out ways to improve them. This review highlights why Saccharomyces cerevisiae remains a crucial player for large-scale bioethanol production from lignocellulose and discusses the potential of genome shuffling to create even more efficient yeast strains.

Engineered Saccharomyces cerevisiae harbors xylose isomerase and xylose transporter improves co-fermentation of xylose and glucose for ethanol production

Saccharomyces cerevisiae cannot assimilate xylose, second to glucose derived from lignocellulosic biomass. Here, the engineered S. cerevisiae strains INVSc-XI and INVSc-XI/XT were constructed using xylA and Xltr1p to co-utilize xylose and glucose, achieving economic viability and sustainable production of fuels. The xylose utilization rate of INVSc-XI/XT was 2.3-fold higher than that of INVSc-XI, indicating that overexpressing Xltr1p could further enhance xylose utilization. In mixed sugar media, a small amount of glucose enhanced the consumption of xylose by INVSc-XI/XT. Transcriptome analysis showed that glucose increased the upregulation of acetate of coenzyme A synthetase (ACS), alcohol dehydrogenase (ADH), and transketolase (TKL) gene expression in INVSc-XI/XT, further promoting xylose utilization and ethanol yield. The highest ethanol titer of 2.91 g/L with a yield of 0.29 g/g at 96 h by INVSc-XI/XT was 56.9% and 63.0% of the theoretical ethanol yield from glucose and xylose, respectively. These results showed overexpression of xylA and Xltr1p is a promising strategy for improving xylose and glucose conversion to ethanol. Although the ability of strain INVSc-XI/XT to produce ethanol was not very satisfactory, glucose was discovered to influence xylose utilization in strain INVSc-XI/XT. Altering the glucose concentration is a promising strategy to improve the xylose and glucose co-utilization.

Development of a Robust Saccharomyces cerevisiae Strain for Efficient Co-Fermentation of Mixed Sugars and Enhanced Inhibitor Tolerance through Protoplast Fusion

The economical and efficient commercial production of second-generation bioethanol requires fermentation microorganisms capable of entirely and rapidly utilizing all sugars in lignocellulosic hydrolysates. In this study, we developed a recombinant Saccharomyces cerevisiae strain, BLH510, through protoplast fusion and metabolic engineering to enhance its ability to co-ferment glucose, xylose, cellobiose, and xylooligosaccharides while tolerating various inhibitors commonly found in lignocellulosic hydrolysates. The parental strains, LF1 and BLN26, were selected for their superior glucose/xylose co-fermentation capabilities and inhibitor tolerance, respectively. The fusion strain BLH510 demonstrated efficient utilization of mixed sugars and high ethanol yield under oxygen-limited conditions. Under low inoculum conditions, strain BLH510 could completely consume all four kinds of sugars in the medium within 84 h. The fermentation produced 33.96 g/L ethanol, achieving 84.3% of the theoretical ethanol yield. Despite the challenging presence of mixed inhibitors, BLH510 successfully metabolized all four sugars above after 120 h of fermentation, producing approximately 30 g/L ethanol and reaching 83% of the theoretical yield. Also, strain BLH510 exhibited increased intracellular trehalose content, particularly under conditions with mixed inhibitors, where the intracellular trehalose reached 239.3 mg/g yeast biomass. This elevated trehalose content contributes to the enhanced stress tolerance of BLH510. The study also optimized conditions for protoplast preparation and fusion, balancing high preparation efficiency and satisfactory regeneration efficiency. The results indicate that BLH510 is a promising candidate for industrial second-generation bioethanol production from lignocellulosic biomass, offering improved performance under challenging fermentation conditions. Our work demonstrates the potential of combining protoplast fusion and metabolic engineering to develop superior S. cerevisiae strains for lignocellulosic bioethanol production. This approach can also be extended to develop robust microbial platforms for producing a wide array of lignocellulosic biomass-based biochemicals.

Co-conversion of lignocellulose-derived glucose, xylose, and aromatics to polyhydroxybutyrate by metabolically engineered Cupriavidus necator

Utilization of all major components of lignocellulose is essential for biomass biorefining. Glucose, xylose, and lignin-derived aromatics can be generated from cellulose, hemicellulose, and lignin of lignocellulose degradation through pretreatment and hydrolysis. In present work, Cupriavidus necator H16 was engineered to utilize glucose, xylose, p-coumaric acid, and ferulic acid simultaneously by multi-step genetic engineering. Firstly, genetic modification and adaptive laboratory evolution were performed to promote glucose transmembrane transport and metabolism. Xylose metabolism was then engineered by integrating genes xylAB (xylose isomerase and xylulokinase) and xylE (proton-coupled symporter) in the locus of ldh (lactate dehydrogenase) and ackA (acetate kinase) on the genome, respectively. Thirdly, p-coumaric acid and ferulic acid metabolism was achieved by constructing an exogenous CoA-dependent non-β-oxidation pathway. Using corn stover hydrolysates as carbon sources, the resulting engineered strain Reh06 simultaneously converted all components of glucose, xylose, p-coumaric acid, and ferulic acid to produce 11.51 g/L polyhydroxybutyrate.

Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates

Issatchenkia orientalis, exhibiting high tolerance against harsh environmental conditions, is a promising metabolic engineering host for producing fuels and chemicals from cellulosic hydrolysates containing fermentation inhibitors under acidic conditions. Although genetic tools for I. orientalis exist, they require auxotrophic mutants so that the selection of a host strain is limited. We developed a drug resistance gene (cloNAT)-based genome-editing method for engineering any I. orientalis strains and engineered I. orientalis strains isolated from various sources for xylose fermentation. Specifically, xylose reductase, xylitol dehydrogenase, and xylulokinase from Scheffersomyces stipitis were integrated into an intended chromosomal locus in four I. orientalis strains (SD108, IO21, IO45, and IO46) through Cas9-based genome editing. The resulting strains (SD108X, IO21X, IO45X, and IO46X) efficiently produced ethanol from cellulosic and hemicellulosic hydrolysates even though the pH adjustment and nitrogen source were not provided. As they presented different fermenting capacities, selection of a host I. orientalis strain was crucial for producing fuels and chemicals using cellulosic hydrolysates.

Regulatory mechanism of Haa1p and Tye7p in Saccharomyces cerevisiae when fermenting mixed glucose and xylose with or without inhibitors

Background

Various inhibitors coexist in the hydrolysate derived from lignocellulosic biomass. They inhibit the performance of Saccharomyces cerevisiae and further restrict the development of industrial bioethanol production. Transcription factors are regarded as targets for constructing robust S. cerevisiae by genetic engineering. The tolerance-related transcription factors have been successively reported, while their regulatory mechanisms are not clear. In this study, we revealed the regulation mechanisms of Haa1p and Tye7p that had outstanding contributions to the improvement of the fermentation performance and multiple inhibitor tolerance of S. cerevisiae.

Results

Comparative transcriptomic analyses were applied to reveal the regulatory mechanisms of Haa1p and Tye7p under mixed sugar fermentation conditions with mixed inhibitors [acetic acid and furfural (AFur)] or without inhibitor (C) using the original strain s6 (S), the HAA1-overexpressing strain s6H3 (H), and the TYE7-overexpressing strain s6T3 (T). The expression of the pathways related to carbohydrate, amino acid, transcription, translation, cofactors, and vitamins metabolism was enhanced in the strains s6H3 and s6T3. Compared to C_H vs. C_S group, the unique DEGs in AFur_H vs. AFur_S group were further involved in oxidative phosphorylation, purine metabolism, vitamin B6 metabolism, and spliceosome under the regulation of Haa1p. A similar pattern appeared under the regulation of Tye7p, and the unique DEGs in AFur_T vs. AFur_S group were also involved in riboflavin metabolism and spliceosome. The most significant difference between the regulations of Haa1p and Tye7p was the intracellular energy supply. Haa1p preferred to enhance oxidative phosphorylation, while Tye7p tended to upregulate glycolysis/gluconeogenesis.

Conclusions

Global gene expressions could be rewired with the overexpression of HAA1 or TYE7. The positive perturbations of energy and amino acid metabolism were beneficial to the improvement of the fermentation performance of the strain. Furthermore, strengthening of key cofactor metabolism, and transcriptional and translational regulation were helpful in improving the strain tolerance. This work provides a novel and comprehensive understanding of the regulation mechanisms of Haa1p and Tye7p in S. cerevisiae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01822-4.

Response mechanisms of Saccharomyces cerevisiae to the stress factors present in lignocellulose hydrolysate and strategies for constructing robust strains

Bioconversion of lignocellulosic biomass to biofuels such as bioethanol and high value-added products has attracted great interest in recent decades due to the carbon neutral nature of biomass feedstock. However, there are still many key technical difficulties for the industrial application of biomass bioconversion processes. One of the challenges associated with the microorganism Saccharomyces cerevisiae that is usually used for bioethanol production refers to the inhibition of the yeast by various stress factors. These inhibitive effects seriously restrict the growth and fermentation performance of the strains, resulting in reduced bioethanol production efficiency. Therefore, improving the stress response ability of the strains is of great significance for industrial production of bioethanol. In this article, the response mechanisms of S. cerevisiae to various hydrolysate-derived stress factors including organic acids, furan aldehydes, and phenolic compounds have been reviewed. Organic acids mainly stimulate cells to induce intracellular acidification, furan aldehydes mainly break the intracellular redox balance, and phenolic compounds have a greater effect on membrane homeostasis. These damages lead to inadequate intracellular energy supply and dysregulation of transcription and translation processes, and then activate a series of stress responses. The regulation mechanisms of S. cerevisiae in response to these stress factors are discussed with regard to the cell wall/membrane, energy, amino acids, transcriptional and translational, and redox regulation. The reported key target genes and transcription factors that contribute to the improvement of the strain performance are summarized. Furthermore, the genetic engineering strategies of constructing multilevel defense and eliminating stress effects are discussed in order to provide technical strategies for robust strain construction. It is recommended that robust S. cerevisiae can be constructed with the intervention of metabolic regulation based on the specific stress responses. Rational design with multilevel gene control and intensification of key enzymes can provide good strategies for construction of robust strains.

Spent mushroom substrates for ethanol production - Effect of chemical and structural factors on enzymatic saccharification and ethanolic fermentation of Lentinula edodes-pretreated hardwood

Spent mushroom substrates (SMS) from cultivation of shiitake (Lentinula edodes) on three hardwood species were investigated regarding their potential for cellulose saccharification and for ethanolic fermentation of the produced hydrolysates. High glucan digestibility was achieved during enzymatic saccharification of the SMSs, which was related to the low mass fractions of lignin and xylan, and it was neither affected by the relative content of lignin guaiacyl units nor the substrate crystallinity. The high nitrogen content in SMS hydrolysates, which was a consequence of the fungal pretreatment, was positive for the fermentation, and it ensured ethanol yields corresponding to 84-87% of the theoretical value in fermentations without nutrient supplementation. Phenolic compounds and acetic acid were detected in the SMS hydrolysates, but due to their low concentrations, the inhibitory effect was limited. The solid leftovers resulting from SMS hydrolysis and the fermentation residues were quantified and characterized for further valorisation.

Glucose Isomerase: Functions, Structures, and Applications

Glucose isomerase (GI, also known as xylose isomerase) reversibly isomerizes D-glucose and D-xylose to D-fructose and D-xylulose, respectively. GI plays an important role in sugar metabolism, fulfilling nutritional requirements in bacteria. In addition, GI is an important industrial enzyme for the production of high-fructose corn syrup and bioethanol. This review introduces the functions, structure, and applications of GI, in addition to presenting updated information on the characteristics of newly discovered GIs and structural information regarding the metal-binding active site of GI and its interaction with the inhibitor xylitol. This review provides an overview of recent advancements in the characterization and engineering of GI, as well as its industrial applications, and will help to guide future research in this field.

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

BACKGROUND

Efficient use of glucose and xylose is a key for the economic production of lignocellulosic biofuels and biochemicals, and different recombinant strains have been constructed for xylose utilization including those using Zymomonas mobilis as the host. However, the xylose utilization efficiency still needs to be improved. In this work, the strategy of combining metabolic engineering and adaptive laboratory evolution (ALE) was employed to develop recombinant Z. mobilis strains that can utilize xylose efficiently at high concentrations, and NGS-based genome resequencing and RNA-Seq transcriptomics were performed for strains evolved after serial transfers in different media to understand the impact of xylose and differences among strains with different xylose-utilization capabilities at molecular level.

RESULTS

Heterologous genes encoding xylose isomerase and xylulokinase were evaluated, which were then introduced into xylose-utilizing strain Z. mobilis 8b to enhance its capacity of xylose utilization. The results demonstrated that the effect of three xylose isomerases on xylose utilization was different, and the increase of copy number of xylose metabolism genes can improve xylose utilization. Among various recombinant strains constructed, the xylose utilization capacity of the recombinant strain 8b-RsXI-xylB was the best, which was further improved through continuous adaption with 38 transfers over 100 days in 50 g/L xylose media. The fermentation performances of the parental strain 8b, the evolved 8b-S38 strain with the best xylose utilization capability, and the intermediate strain 8b-S8 in different media were compared, and the results showed that only 8b-S38 could completely consume xylose at 50 g/L and 100 g/L concentrations. In addition, the xylose consumption rate of 8b-S38 was faster than that of 8b at different xylose concentrations from 50 to 150 g/L, and the ethanol yield increased by 16 ~ 40%, respectively. The results of the mixed-sugar fermentation also demonstrated that 8b-S38 had a higher xylose consumption rate than 8b, and its maximum ethanol productivity was 1.2 ~ 1.4 times higher than that of 8b and 8b-S8. Whole-genome resequencing identified three common genetic changes in 8b-S38 compared with 8b and 8b-S8. RNA-Seq study demonstrated that the expression levels of genes encoding chaperone proteins, ATP-dependent proteases, phage shock proteins, ribosomal proteins, flagellar operons, and transcriptional regulators were significantly increased in xylose media in 8b-S38. The up-regulated expression of these genes may therefore contribute to the efficient xylose utilization of 8b-S38 by maintaining the normal cell metabolism and growth, repairing cellular damages, and rebalancing cellular energy to help cells resist the stressful environment.

CONCLUSIONS

This study provides gene candidates to improve xylose utilization, and the result of expressing an extra copy of xylose isomerase and xylulokinase improved xylose utilization also provides a direction for efficient xylose-utilization strain development in other microorganisms. In addition, this study demonstrated the necessity to combine metabolic engineering and ALE for industrial strain development. The recombinant strain 8b-S38 can efficiently metabolize xylose for ethanol fermentation at high xylose concentrations as well as in mixed sugars of glucose and xylose, which could be further developed as the microbial biocatalyst for the production of lignocellulosic biofuels and biochemicals.

Directed evolution and secretory expression of xylose isomerase for improved utilisation of xylose in Saccharomyces cerevisiae

BACKGROUND

Xylose contained in lignocellulosic biomass is an attractive carbon substrate for economically viable conversion to bioethanol. Extensive research has been conducted on xylose fermentation using recombinant Saccharomyces cerevisiae expressing xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways along with the introduction of a xylose transporter and amplification of the downstream pathway. However, the low utilization of xylose in the presence of glucose, due to the varying preference for cellular uptake, is a lingering challenge. Studies so far have mainly focused on xylose utilization inside the cells, but there have been little trials on the conversion of xylose to xylulose by cell before uptake. We hypothesized that the extracellular conversion of xylose to xylulose before uptake would facilitate better utilization of xylose even in the presence of glucose. To verify this, XI from Piromyces sp. was engineered and hyper-secreted in S. cerevisiae for the extracellular conversion of xylose to xylulose.

RESULTS

The optimal pH of XI was lowered from 7.0 to 5.0 by directed evolution to ensure its high activity under the acidic conditions used for yeast fermentation, and hyper-secretion of an engineered XI-76 mutant (E56A and I252M) was accomplished by employing target protein-specific translational fusion partners. The purified XI-76 showed twofold higher activity than that of the wild type at pH 5. The secretory expression of XI-76 in the previously developed xylose utilizing yeast strain, SR8 increased xylose consumption and ethanol production by approximately 7-20% and 15-20% in xylose fermentation and glucose and xylose co-fermentation, respectively.

CONCLUSIONS

Isomerisation of xylose to xylulose before uptake using extracellular XI was found to be effective in xylose fermentation or glucose/xylose co-fermentation. This suggested that glucose competed less with xylulose than with xylose for uptake by the cell. Consequently, the engineered XI secretion system constructed in this study can pave the way for simultaneous utilization of C5/C6 sugars from the sustainable lignocellulosic biomass.

Improving Acetic Acid and Furfural Resistance of Xylose-Fermenting Saccharomyces cerevisiae Strains by Regulating Novel Transcription Factors Revealed via Comparative Transcriptomic Analysis

Acetic acid and furfural are the two prevalent inhibitors coexisting with glucose and xylose in lignocellulosic hydrolysate. The transcriptional regulations of Saccharomyces cerevisiae in response to acetic acid (Aa), furfural (Fur), and the mixture of acetic acid and furfural (Aa_Fur) were revealed during mixed glucose and xylose fermentation. Carbohydrate metabolism pathways were significantly enriched in response to Aa, while pathways of xenobiotic biodegradation and metabolism were significantly enriched in response to Fur. In addition to these pathways, other pathways were activated in response to Aa_Fur, i.e., cofactor and vitamin metabolism and lipid metabolism. Overexpression of Haa1p or Tye7p improved xylose consumption rates by nearly 50%, while the ethanol yield was enhanced by nearly 8% under acetic acid and furfural stress conditions. Co-overexpression of Haa1p and Tye7p resulted in a 59% increase in xylose consumption rate and a 12% increase in ethanol yield, revealing the beneficial effects of Haa1p and Tye7p on improving the tolerance of yeast to mixed acetic acid and furfural.IMPORTANCE Inhibitor tolerance is essential for S. cerevisiae when fermenting lignocellulosic hydrolysate with various inhibitors, including weak acids, furans, and phenols. The details regarding how xylose-fermenting S. cerevisiae strains respond to multiple inhibitors during fermenting mixed glucose and xylose are still unknown. This study revealed the transcriptional regulation mechanism of an industrial xylose-fermenting S. cerevisiae strain in response to acetic acid and furfural. The transcription factor Haa1p was found to be involved in both acetic acid and furfural tolerance. In addition to Haa1p, four other transcription factors, Hap4p, Yox1p, Tye7p, and Mga1p, were identified as able to improve the resistance of yeast to these two inhibitors. This study underscores the feasibility of uncovering effective transcription factors for constructing robust strains for lignocellulosic bioethanol production.

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.

Chemical Pretreatments on Residual Cocoa Pod Shell Biomass for Bioethanol Production

Cocoa pod shell is an essential agricultural residue in Ecuador, and this study addressed its potential valorization for bioethanol production. For this, three types of pretreatments, acid, alkaline, and autohydrolysis, were applied to pod shells from two different cocoa types, national and CCN-51. to remove the lignin. Untreated and treated biomasses were characterized by composition, thermal stability, Fourier transformed infrared spectroscopy (FITR), and scanning electron microscopy (SEM). The treated biomass was then enzymatically hydrolyzed with cellulase. Reducing sugars were quantified after pretreatments and enzymatic hydrolysis, and the pretreatment liquors and the enzymatic hydrolysates were subjected to alcoholic fermentation with Saccharomyces cerevisiae. There were substantial differences in composition between both biomasses, particularly in lignin content, with national cocoa having the lowest values. All pretreatment conditions had significant effects on biomass composition, structure, and thermal properties. After alkaline pretreatment, the biomass presented the highest cellulose and lowest lignin contents, resulting in the highest reducing sugar concentration in the pretreatment liquor. The highest lignin content was found after the acid pretreatment, which resulted in low, reducing sugar concentrations. Autohydrolysis produced similar results as the acid pretreatment; however, it resulted in the highest sugar concentration after enzymatic hydrolysis, while the acid-treated sample had negligible levels. After fermentation, there were no differences in productivity among the pretreatment liquors, but autohydrolysis had the largest ethanol yield. In the hydrolysates, it was also autohydrolysis that resulted in higher productivity and yield. Thus, there is an indication of the formation of inhibitors, both enzymatic activity and ethanol production, in the acid and alkaline pretreatments, and this should be tackled in future research. Nonetheless, given the crucial changes observed in biomass, we believe that cocoa pod shell pretreatment has potential for the generation of reducing sugars that could be further used in different bioprocesses, nor only bioethanol production.

Agro-Food Residues and Bioethanol Potential: A Study for a Specific Area

Bioethanol obtained from agro-food wastes could contribute to decrease the dependency on fossil resources, reduce the impact of fossil fuels on the environment, and mitigate the food versus fuel debate. This study is aimed to investigate the availability of residual inexpensive agro-food biomasses that could feed a second-generation bioethanol plant located in a specific area of North Eastern Italy. After the identification of all crops in the area, more than 40 agro-food residues were analyzed for their availability and compositions in terms of water, polysaccharides, and sugars potentially convertible into bioethanol. 574,166 Mg of residual wet lignocellulosic biomass corresponding to 297,325 Mg of dry material were found available for bioethanol conversion. The most promising substrates were wheat straw and vine shoots. Based on the chemical composition of residues, the potential attainable ethanol was determined. Theoretical potential ethanol production was estimated at nearly 72,000 Mg per year. This quantity extensively exceeds the minimum yearly capacity of a sustainable bioethanol plant previously identified as around 50,000 Mg of ethanol. Taken together, these results demonstrate that, in the analyzed area, agro-food residues are available in an amount that could sustain bioethanol production in a specific and restricted district. Techno-economical evaluations are in progress to assess the actual feasibility of installing a second generation bioethanol production plant in the area of interest.

A Whole-Slurry Fermentation Approach to High-Solid Loading for Bioethanol Production from Corn Stover

Corn stover is the most produced byproduct from maize worldwide. Since it is generated as a residue from maize harvesting, it is an inexpensive and interesting crop residue to be used as a feedstock. An ecologically friendly pretreatment such as autohydrolysis was selected for the manufacture of second-generation bioethanol from corn stover via whole-slurry fermentation at high-solid loadings. Temperatures from 200 to 240 °C were set for the autohydrolysis process, and the solid and liquid phases were analyzed. Additionally, the enzymatic susceptibility of the solid phases was assessed to test the suitability of the pretreatment. Afterward, the production of bioethanol from autohydrolyzed corn stover was carried out, mixing the solid with different percentages of the autohydrolysis liquor (25%, 50%, 75%, and 100%) and water (0% of liquor), from a total whole slurry fermentation (saving energy and water in the liquid–solid separation and subsequent washing of the solid phase) to employing water as only liquid medium. In spite of the challenging scenario of using the liquor fraction as liquid phase in the fermentation, values between 32.2 and 41.9 g ethanol/L and ethanol conversions up to 80% were achieved. This work exhibits the feasibility of corn stover for the production of bioethanol via a whole-slurry fermentation process.

Comparative study of biorefinery processes for the valorization of fast-growing Paulownia wood

In this work, valorization of Paulownia wood (PW) was proposed following several process configurations for biofuels and value-added compounds production. Firstly, autohydrolysis and ethanol-organosolv strategies were assessed separately for the fractionation of PW to enhance the enzymatic digestibility of cellulose. A third strategy focused on a sequential process (autohydrolysis and organosolv) was explored. Two temperatures were selected for the first stage of the combined process. High concentration of oligosaccharides (26.29 g/L) and high concentration of degradation products (17.21 g/L) were obtained at 210 and 230 °C, respectively. The solids obtained from both pretreatments were subjected to organosolv delignification (200 °C, 3 h and 50% ethanol) achieving delignification of 58 and 30% for the autohydrolyzed biomass at 210 °C and 230 °C, respectively. The combined process resulted in susceptible biomass able to produce 64 g/L of ethanol. Therefore, the strategies explored in this work open the possibility to build a refinery around Paulownia wood.

Production of bioethanol and xylitol from non-detoxified corn cob via a two-stage fermentation strategy

A novel two-stage fermentation strategy was applied to produce xylitol and ethanol from the whole acid-pretreated corn cob slurry. The acid-pretreated corn cob was used without filtration and detoxification by the two-stage fermentation with the robust Kluyveromyces marxianus CICC 1727-5. In the first stage, xylose in the slurry after dilute acid pretreatment of lignocellulosic biomass was used to produce xylitol under micro-aeration conditions. In the second stage, simultaneous saccharification fermentation was carried out, and the ethanol was produced from glucose releasing from the solid. Important parameters, such as aeration rate, cellulase loading during xylose utilization and SSF fermentation were studied for best performance. The two-stage fermentation strategy removed the inhibition of glucose on xylose, and little xylose was left in the fermentation broth. Under the optimized condition, the maximum ethanol and xylitol concentration were 52 g/L and 24.2 g/L corresponding to the yield of 0.41 g/g and 0.82 g/g, respectively.

High Gravity Fermentation of Sugarcane Bagasse Hydrolysate by Saccharomyces pastorianus to Produce Economically Distillable Ethanol Concentrations: Necessity of Medium Components Examined

A major economic obstacle in lignocellulosic ethanol production is the low sugar concentrations in the hydrolysate and subsequent fermentation to economically distillable ethanol concentrations. We have previously demonstrated a two-stage fermentation process that recycles xylose with xylose isomerase to increase ethanol productivity, where the low sugar concentrations in the hydrolysate limit the final ethanol concentrations. In this study, three approaches are combined to increase ethanol concentrations. First, the medium-additive requirements were investigated to reduce ethanol dilution. Second, methods to increase the sugar concentrations in the sugarcane bagasse hydrolysate were undertaken. Third, the two-stage fermentation process was recharacterized with high gravity hydrolysate. It was determined that phosphate and magnesium sulfate are essential to the ethanol fermentation. Additionally, the Escherichia coli extract and xylose isomerase additions were shown to significantly increase ethanol productivity. Finally, the fermentation on hydrolysate had only slightly lower productivity than the reagent-grade sugar fermentation; however, both fermentations had similar final ethanol concentrations. The present work demonstrates the capability to produce ethanol from high gravity sugarcane bagasse hydrolysate using Saccharomyces pastorianus with low yeast inoculum in minimal medium. Moreover, ethanol productivities were on par with pilot-scale commercial starch-based facilities, even when the yeast biomass production stage was included.

Improved simultaneous co-fermentation of glucose and xylose by Saccharomyces cerevisiae for efficient lignocellulosic biorefinery

BACKGROUND

Lignocellulosic biorefinery offers economical and sustainable production of fuels and chemicals. Saccharomyces cerevisiae, a promising industrial host for biorefinery, has been intensively developed to expand its product profile. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery.

RESULTS

In this study, we developed a powerful mixed-sugar co-fermenting strain of S. cerevisiae, XUSEA, with improved xylose conversion capacity during simultaneous glucose/xylose co-fermentation. To reinforce xylose catabolism, the overexpression target in the pentose phosphate pathway was selected using a DNA assembler method and overexpressed increasing xylose consumption and ethanol production by twofold. The performance of the newly engineered strain with improved xylose catabolism was further boosted by elevating fermentation temperature and thus significantly reduced the co-fermentation time by half. Through combined efforts of reinforcing the pathway of xylose catabolism and elevating the fermentation temperature, XUSEA achieved simultaneous co-fermentation of lignocellulosic hydrolysates, composed of 39.6 g L^-1 glucose and 23.1 g L^-1 xylose, within 24 h producing 30.1 g L^-1 ethanol with a yield of 0.48 g g^-1.

CONCLUSIONS

Owing to its superior co-fermentation performance and ability for further engineering, XUSEA has potential as a platform in a lignocellulosic biorefinery toward realizing a more economical and sustainable process for large-scale bioethanol production.

Process optimization and kinetic analysis of malic acid production from crude glycerol using Aspergillus niger

In the present work, optimization of crude glycerol fermentation to produce malic acid by using Aspergillus niger was investigated using response surface methodology and artificial neural network. Kinetic investigation of bioconversion of crude glycerol into malic acid using Aspergillus niger was studied using Monod, Mosser, and Haldane-Andrew models. Crude glycerol concentration, initial pH and yeast extract concentration were found to be significant compounds affecting malic acid production by Aspergillus niger. Both dry cell weight and malic acid titre were found decreased with increase in crude glycerol concentration. Haldane-Andrew model gave the best fit for the production of malic acid from crude glycerol with µ_max of 0.1542 h^-1. The maximum malic acid production obtained under optimum conditions was 92.64 + 1.54 g/L after 192 h from crude glycerol using Aspergillus niger.

Enhanced butyric acid production using mixed biomass of brown algae and rice straw by Clostridium tyrobutyricum ATCC25755

A brown alga Saccharina japonica and rice straw are attractive feedstock for microbial butyric acid production. However, inefficient fermentation of mannitol (a dominant component in S. japonica) and toxicity of inhibitors in lignocellulosic hydrolysate are limitations. This study demonstrated that mixed biomass with S. japonica and rice straw was effective in butyric acid production over those restrictions. Mannitol was consumed only when acetic acid was present. Notably, acetic acid was not produced but consumed along with mannitol. By mixing S. japonica and rice straw to take advantage of glucose and acetic acid in rice straw, Clostridium tyrobutyricum effectively consumed mannitol by utilizing acetic acid in hydrolysate and acetic acid derived from glucose with the enhanced butyric acid production. Furthermore, cell growth was restored owing to the decreased inhibitor concentration. The results demonstrate the potential of butyric acid production from mixed biomass of macroalgae/lignocellulose overcoming the drawbacks of single biomass.

Simultaneous fermentation of biomass-derived sugars to ethanol by a co-culture of an engineered Escherichia coli and Saccharomyces cerevisiae

Microorganisms ferment xylose at high rate only when glucose concentration in the medium falls below a critical level. Since the specific productivity of product is highest during exponential to early stationary phase of growth, a glucose utilization negative ethanologenic E. coli (strain LW419a) was constructed for high rate of xylose fermentation in combination with Turbo yeast. This co-culture fermented all the released sugars in an acid/enzyme-treated sugar cane bagasse slurry (10% solids) to an ethanol titer of 24.9 ± 0.8 g.L^-1 (70% of the theoretical yield) in <30 h. Ethanol titer increased to 48.6 ± 1.04 g.L^-1 (yield, 0.45 g.g^-1 sugars) at a solids content of 20% and the highest rate of xylose consumption was 1.58 ± 0.21 g.L^-1.h^-1. This study demonstrates the potential of a co-culture of strain LW419a and yeast to rapidly ferment all the sugars in pretreated biomass slurries to ethanol at their respective highest rates.

Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways

BACKGROUND

Xylose isomerase (XI) and xylose reductase/xylitol dehydrogenase (XR/XDH) pathways have been extensively used to confer xylose assimilation capacity to Saccharomyces cerevisiae and tackle one of the major bottlenecks in the attainment of economically viable lignocellulosic ethanol production. Nevertheless, there is a lack of studies comparing the efficiency of those pathways both separately and combined. In this work, the XI and/or XR/XDH pathways were introduced into two robust industrial S. cerevisiae strains, evaluated in synthetic media and corn cob hemicellulosic hydrolysate and the results were correlated with the differential enzyme activities found in the xylose-pathway engineered strains.

RESULTS

The sole expression of XI was found to increase the fermentative capacity of both strains in synthetic media at 30 °C and 40 °C: decreasing xylitol accumulation and improving xylose consumption and ethanol production. Similar results were observed in fermentations of detoxified hydrolysate. However, in the presence of lignocellulosic-derived inhibitors, a positive synergistic effect resulted from the expression of both XI and XR/XDH, possibly caused by a cofactor equilibrium between the XDH and furan detoxifying enzymes, increasing the ethanol yield by more than 38%.

CONCLUSIONS

This study clearly shows an advantage of using the XI from Clostridium phytofermentans to attain high ethanol productivities and yields from xylose. Furthermore, and for the first time, the simultaneous utilization of XR/XDH and XI pathways was compared to the single expression of XR/XDH or XI and was found to improve ethanol production from non-detoxified hemicellulosic hydrolysates. These results extend the knowledge regarding S. cerevisiae xylose assimilation metabolism and pave the way for the construction of more efficient strains for use in lignocellulosic industrial processes.

Bioconversion of pentose sugars to value added chemicals and fuels: Recent trends, challenges and possibilities

Most of the crop plants contain about 30% of hemicelluloses comprising D-xylose and D-arabinose. One of the major limitation for the use of pentose sugars is that high purity grade D-xylose and D-arabinose are yet to be produced as commodity chemicals. Research and developmental activities are going on in this direction for their use as platform intermediates through economically viable strategies. During chemical pretreatment of biomass, the pentose sugars were generated in the liquid stream along with other compounds. This contains glucose, proteins, phenolic compounds, minerals and acids other than pentose sugars. Arabinose is present in small amounts, which can be used for the economic production of value added compound, xylitol. The present review discusses the recent trends and developments as well as challenges and opportunities in the utilization of pentose sugars generated from lignocellulosic biomass for the production of value added compounds.

Evaluation of buriti endocarp as lignocellulosic substrate for second generation ethanol production

The production of lignocellulosic ethanol is one of the most promising alternatives to fossil fuels; however, this technology still faces many challenges related to the viability of the lignocellulosic alcohol in the market. In this paper the endocarp of buriti fruit was assessed for ethanol production. The fruit endocarp was characterized physically and chemically. Acid and alkaline pre-treatments were optimized by surface response methodology for removal of hemicellulose and lignin from the biomass. Hemicellulose content was reduced by 88% after acid pretreatment. Alkaline pre-treatment reduced the lignin content in the recovered biomass from 11.8% to 4.2% and increased the concentration of the cellulosic fraction to 88.5%. The pre-treated biomass was saccharified by the action of cellulolytic enzymes and, under optimized conditions, was able to produce 110 g of glucose per L of hydrolyzate. Alcoholic fermentation of the enzymatic hydrolyzate performed by Saccharomyces cerevisiae resulted in a fermented medium with 4.3% ethanol and a yield of product per substrate (YP/S) of 0.33.

Recombinant Diploid Saccharomyces cerevisiae Strain Development for Rapid Glucose and Xylose Co-Fermentation

Cost-effective production of cellulosic ethanol requires robust microorganisms for rapid co-fermentation of glucose and xylose. This study aims to develop a recombinant diploid xylose-fermenting Saccharomyces cerevisiae strain for efficient conversion of lignocellulosic biomass sugars to ethanol. Episomal plasmids harboring codon-optimized Piromyces sp. E2 xylose isomerase (PirXylA) and Orpinomyces sp. ukk1 xylose (OrpXylA) genes were constructed and transformed into S. cerevisiae. The strain harboring plasmids with tandem PirXylA was favorable for xylose utilization when xylose was used as the sole carbon source, while the strain harboring plasmids with tandem OrpXylA was beneficial for glucose and xylose cofermentation. PirXylA and OrpXylA genes were also individually integrated into the genome of yeast strains in multiple copies. Such integration was beneficial for xylose alcoholic fermentation. The respiration-deficient strain carrying episomal or integrated OrpXylA genes exhibited the best performance for glucose and xylose co-fermentation. This was partly attributed to the high expression levels and activities of xylose isomerase. Mating a respiration-efficient strain carrying the integrated PirXylA gene with a respiration-deficient strain harboring integrated OrpXylA generated a diploid recombinant xylose-fermenting yeast strain STXQ with enhanced cell growth and xylose fermentation. Co-fermentation of 162 g L−1 glucose and 95 g L−1 xylose generated 120.6 g L−1 ethanol in 23 h, with sugar conversion higher than 99%, ethanol yield of 0.47 g g−1, and ethanol productivity of 5.26 g L−1·h−1.

Review of Second Generation Bioethanol Production from Residual Biomass

In the context of climate change and the depletion of fossil fuels, there is a great need for alternatives to petroleum in the transport sector. This review provides an overview of the production of second generation bioethanol, which is distinguished from the first generation and subsequent generations of biofuels by its use of lignocellulosic biomass as raw material. The structural components of the lignocellulosic biomass such as cellulose, hemicellulose and lignin, are presented along with technological unit steps including pretreatment, enzymatic hydrolysis, fermentation, distillation and dehydration. The purpose of the pretreatment step is to increase the surface area of carbohydrate available for enzymatic saccharification, while minimizing the content of inhibitors. Performing the enzymatic hydrolysis releases fermentable sugars, which are converted by microbial catalysts into ethanol. The hydrolysates obtained after the pretreatment and enzymatic hydrolysis contain a wide spectrum of sugars, predominantly glucose and xylose. Genetically engineered microorganisms are therefore needed to carry out co-fermentation. The excess of harmful inhibitors in the hydrolysate, such as weak organic acids, furan derivatives and phenol components, can be removed by detoxification before fermentation. Effective saccharification further requires using exogenous hemicellulases and cellulolytic enzymes. Conventional species of distiller's yeast are unable to ferment pentoses into ethanol, and only a very few natural microorganisms, including yeast species like Candida shehatae, Pichia (Scheffersomyces) stipitis, and Pachysolen tannophilus, metabolize xylose to ethanol. Enzymatic hydrolysis and fermentation can be performed in a number of ways: by separate saccharification and fermentation, simultaneous saccharification and fermentation or consolidated bioprocessing. Pentose-fermenting microorganisms can be obtained through genetic engineering, by introducing xylose-encoding genes into metabolism of a selected microorganism to optimize its use of xylose accumulated in the hydrolysate.

Engineering xylose metabolism for production of polyhydroxybutyrate in the non-model bacterium Burkholderia sacchari

Background

Despite its ability to grow and produce high-value molecules using renewable carbon sources, two main factors must be improved to use Burkholderia sacchari as a chassis for bioproduction at an industrial scale: first, the lack of molecular tools to engineer this organism and second, the inherently slow growth rate and poly-3-hydroxybutyrate [P(3HB)] production using xylose. In this work, we have addressed both factors.

Results

First, we adapted a set of BglBrick plasmids and showed tunable expression in B. sacchari. Finally, we assessed growth rate and P(3HB) production through overexpression of xylose transporters, catabolic or regulatory genes. Overexpression of xylR significantly improved growth rate (55.5% improvement), polymer yield (77.27% improvement), and resulted in 71% of cell dry weight as P(3HB).

Conclusions

These values are unprecedented for P(3HB) accumulation using xylose as a sole carbon source and highlight the importance of precise expression control for improving utilization of hemicellulosic sugars in B. sacchari.

Largely enhanced bioethanol production through the combined use of lignin-modified sugarcane and xylose fermenting yeast strain

The recalcitrant structure of lignocellulosic biomass is a major barrier in efficient biomass-to-ethanol bioconversion processes. The combination of feedstock engineering via modification in the lignin synthesis pathway of sugarcane and co-fermentation of xylose and glucose with a recombinant xylose utilizing yeast strain produced 148% more ethanol compared to that of the wild type biomass and control strain. The lignin reduced biomass led to a substantially increased release of fermentable sugars (glucose and xylose). The engineered yeast strain efficiently co-utilized glucose and xylose for fermentation, elevating ethanol yields. In this study, it was experimentally demonstrated that the combined efforts of engineering both feedstock and microorganisms largely enhances the bioconversion of lignocellulosic feedstock to bioethanol. This strategy will significantly improve the economic feasibility of lignocellulosic biofuels production.

Genomic and phenotypic characterization of a refactored xylose-utilizing Saccharomyces cerevisiae strain for lignocellulosic biofuel production

BACKGROUND

Engineered strains of Saccharomyces cerevisiae have significantly improved the prospects of biorefinery by improving the bioconversion yields in lignocellulosic bioethanol production and expanding the product profiles to include advanced biofuels and chemicals. However, the lignocellulosic biorefinery concept has not been fully applied using engineered strains in which either xylose utilization or advanced biofuel/chemical production pathways have been upgraded separately. Specifically, high-performance xylose-fermenting strains have rarely been employed as advanced biofuel and chemical production platforms and require further engineering to expand their product profiles.

RESULTS

In this study, we refactored a high-performance xylose-fermenting S. cerevisiae that could potentially serve as a platform strain for advanced biofuels and biochemical production. Through combinatorial CRISPR-Cas9-mediated rational and evolutionary engineering, we obtained a newly refactored isomerase-based xylose-fermenting strain, XUSE, that demonstrated efficient conversion of xylose into ethanol with a high yield of 0.43 g/g. In addition, XUSE exhibited the simultaneous fermentation of glucose and xylose with negligible glucose inhibition, indicating the potential of this isomerase-based xylose-utilizing strain for lignocellulosic biorefinery. The genomic and transcriptomic analysis of XUSE revealed beneficial mutations and changes in gene expression that are responsible for the enhanced xylose fermentation performance of XUSE.

CONCLUSIONS

In this study, we developed a high-performance xylose-fermenting S. cerevisiae strain, XUSE, with high ethanol yield and negligible glucose inhibition. Understanding the genomic and transcriptomic characteristics of XUSE revealed isomerase-based engineering strategies for improved xylose fermentation in S. cerevisiae. With high xylose fermentation performance and room for further engineering, XUSE could serve as a promising platform strain for lignocellulosic biorefinery.

Enhanced biosynthesis of 3,4-dihydroxybutyric acid by engineered Escherichia coli in a dual-substrate system

3,4-Dihydroxybutyric acid (3,4-DHBA), a versatile platform four carbon (C4) chemical, can be used as a precursor in the production of many commercially important chemicals. Here, a dual-substrate biosynthesis system was developed for 3,4-DHBA production via a synthetic pathway established in an engineered Escherichia coli, and using xylose as a synthetic substrate and glucose as a cell growth substrate. The deletion of genes xylA, yjhH and yagE and others encoding for alcohol dehydrogenases in E. coli is essential for the production of 3,4-DHBA. Blocking competing pathway by removing the gene yiaE encoding for a 2-keto-3-deoxy-D-xylonate reductase also facilitated carbon flow towards the synthesis of 3,4-DHBA. Furthermore, regulation the availability of NAD⁺ resulted in further improved 3,4-DHBA production. The combinational optimization of the biosynthesis system led to a production of 0.38g/L 3,4-DHBA. This study provides an alternative 3,4-DHBA biosynthesis approach with the possibility of utilizing hydrolysates of lignocellulosic biomass as substrates.

Advances in cellulosic conversion to fuels: engineering yeasts for cellulosic bioethanol and biodiesel production

Cellulosic fuels are expected to have great potential industrial applications in the near future, but they still face technical challenges to become cost-competitive fuels, thus presenting many opportunities for improvement. The economical production of viable biofuels requires metabolic engineering of microbial platforms to convert cellulosic biomass into biofuels with high titers and yields. Fortunately, integrating traditional and novel engineering strategies with advanced engineering toolboxes has allowed the development of more robust microbial platforms, thus expanding substrate ranges. This review highlights recent trends in the metabolic engineering of microbial platforms, such as the industrial yeasts Saccharomyces cerevisiae and Yarrowia lipolytica, for the production of renewable fuels.

Construction of efficient xylose-fermenting Saccharomyces cerevisiae through a synthetic isozyme system of xylose reductase from Scheffersomyces stipitis

Engineered Saccharomyces cerevisiae has been used for ethanol production from xylose, the abundant sugar in lignocellulosic hydrolyzates. Development of engineered S. cerevisiae able to utilize xylose effectively is crucial for economical and sustainable production of fuels. To this end, the xylose-metabolic genes (XYL1, XYL2 and XYL3) from Scheffersomyces stipitis have been introduced into S. cerevisiae. The resulting engineered S. cerevisiae strains, however, often exhibit undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. This work was undertaken to construct an improved xylose-fermenting strain by developing a synthetic isozyme system of xylose reductase (XR). The DXS strain having both wild XR and mutant XR showed low xylitol accumulation and fast xylose consumption compared to the engineered strains expressing only one type of XRs, resulting in improved ethanol yield and productivity. These results suggest that the introduction of the XR-based synthetic isozyme system is a promising strategy to develop efficient xylose-fermenting strains.

Integrated approach for selecting efficient Saccharomyces cerevisiae for industrial lignocellulosic fermentations: Importance of yeast chassis linked to process conditions

In this work, four robust yeast chassis isolated from industrial environments were engineered with the same xylose metabolic pathway. The recombinant strains were physiologically characterized in synthetic xylose and xylose-glucose medium, on non-detoxified hemicellulosic hydrolysates of fast-growing hardwoods (Eucalyptus and Paulownia) and agricultural residues (corn cob and wheat straw) and on Eucalyptus hydrolysate at different temperatures. Results show that the co-consumption of xylose-glucose was dependent on the yeast background. Moreover, heterogeneous results were obtained among different hydrolysates and temperatures for each individual strain pointing to the importance of designing from the very beginning a tailor-made yeast considering the specific raw material and process.

Valorization of exhausted sugar beet cossettes by successive hydrolysis and two fermentations for the production of bio-products

Exhausted sugar beet cossettes (ESBC) show an enormous potential as a source of sugars for the production of bio-products. Enzyme hydrolysis with the combined effect of mainly cellulases, xylanases and pectinases, turned out to be very efficient, obtaining almost double the concentration of sugars measured with the sole action of Celluclast® and β-glucosidase, and increasing 5 times the hydrolysis rate. As the sole pretreatment, ESBC soaked in the hydrolysis buffer were autoclaved, avoiding the application of severe conventional biomass pretreatments. Moreover, a promising alternative for the complete utilization of glucose, xylose, arabinose, mannose and maltose contained in ESBC is proposed in this paper. It consists of sequential fermentation of sugars released in the hydrolysis step to produce bioethanol and lactic acid as main bio-products. Compared to separate fermentations, with this strategy glucose and hemicellulose derived sugars were completely consumed and the 44% of pectin derived sugars.

Enhanced fuel ethanol production from rice straw hydrolysate by an inhibitor-tolerant mutant strain of Scheffersomyces stipitis

A novel process for bioethanol production from lignocellulosic biomass using an inhibitor-tolerant mutant strain of Scheffersomyces stipitis and cell-recycling continuous fermentation.

Oxidative production of xylonic acid using xylose in distillation stillage of cellulosic ethanol fermentation broth by Gluconobacter oxydans

An oxidative production process of xylonic acid using xylose in distillation stillage of cellulosic ethanol fermentation broth was designed, experimentally investigated, and evaluated. Dry dilute acid pretreated and biodetoxified corn stover was simultaneously saccharified and fermented into 59.80g/L of ethanol (no xylose utilization). 65.39g/L of xylose was obtained in the distillation stillage without any concentrating step after ethanol was distillated. Then the xylose was completely converted into 66.42g/L of xylonic acid by Gluconobacter oxydans. The rigorous Aspen Plus modeling shows that the wastewater generation and energy consumption was significantly reduced comparing to the previous xylonic acid production process using xylose in pretreatment liquid. This study provided a practical process option for xylonic acid production from lignocellulose feedstock with significant reduction of wastewater and energy consumption.

Effect of manganese ions on ethanol fermentation by xylose isomerase expressing Saccharomyces cerevisiae under acetic acid stress

The efficient fermentation of lignocellulosic hydrolysates in the presence of inhibitors is highly desirable for bioethanol production. Among the inhibitors, acetic acid released during the pretreatment of lignocellulose negatively affects the fermentation performance of biofuel producing organisms. In this study, we evaluated the inhibitory effects of acetic acid on glucose and xylose fermentation by a high performance engineered strain of xylose utilizing Saccharomyces cerevisiae, SXA-R2P-E, harboring a xylose isomerase based pathway. The presence of acetic acid severely decreased the xylose fermentation performance of this strain. However, the acetic acid stress was alleviated by metal ion supplementation resulting in a 52% increased ethanol production rate under 2g/L of acetic acid stress. This study shows the inhibitory effect of acetic acid on an engineered isomerase-based xylose utilizing strain and suggests a simple but effective method to improve the co-fermentation performance under acetic acid stress for efficient bioethanol production.