Engineering a wild-type diploid Saccharomyces cerevisiae strain for second-generation bioethanol production

Highly Efficient Production of Cellulosic Ethanol from Poplar Using an Optimal C6/C5 Co-Fermentation Strain of Saccharomyces cerevisiae

Cellulosic ethanol is the key technology to alleviate the pressure of energy supply and climate change. However, the ethanol production process, which is close to industrial production and has a high saccharification rate and ethanol yield, still needs to be developed. This study demonstrates the effective conversion of poplar wood waste into fuel-grade ethanol. By employing a two-step pretreatment using sodium chlorite (SC)-dilute sulfuric acid (DSA), the raw material achieved a sugar conversion rate exceeding 85% of the theoretical value. Under optimized conditions, brewing yeast co-utilizing C6/C5 enabled a yield of 35 g/L ethanol from 10% solid loading delignified poplar hydrolysate. We increased the solid loading to enhance the final ethanol concentration and optimized both the hydrolysis and fermentation stages. With 20% solid loading delignified poplar hydrolysate, the final ethanol concentration reached 60 g/L, a 71.4% increase from the 10% solid loading. Our work incorporates the pretreatment, enzymatic hydrolysis, and fermentation stages to establish a simple, crude poplar waste fuel ethanol process, expanding the range of feedstocks for second-generation fuel ethanol production.

Construction of an alternative NADPH regeneration pathway improves ethanol production in Saccharomyces cerevisiae with xylose metabolic pathway

Full conversion of glucose and xylose from lignocellulosic hydrolysates is required for obtaining a high ethanol yield. However, glucose and xylose share flux in the pentose phosphate pathway (PPP) and glycolysis pathway (EMP), with glucose having a competitive advantage in the shared metabolic pathways. In this work, we knocked down ZWF1 to preclude glucose from entering the PPP. This reduced the [NADPH] level and disturbed growth on both glucose or xylose, confirming that the oxidative PPP, which begins with Zwf1p and ultimately leads to CO2 production, is the primary source of NADPH in both glucose and xylose. Upon glucose depletion, gluconeogenesis is necessary to generate glucose-6-phosphate, the substrate of Zwf1p. We re-established the NADPH regeneration pathway by replacing the endogenous NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene TDH3 with heterogenous NADP + -GAPDH genes GDH, gapB, and GDP1. Among the resulting strains, the strain BZP1 (zwf1Δ, tdh3::GDP1) exhibited a similar xylose consumption rate before glucose depletion, but a 1.6-fold increased xylose consumption rate following glucose depletion compared to the original strain BSGX001, and the ethanol yield for total consumed sugars of BZP1 was 13.5% higher than BSGX001. This suggested that using the EMP instead of PPP to generate NADPH reduces the wasteful metabolic cycle and excess CO2 release from oxidative PPP. Furthermore, we used a copper-repressing promoter to modulate the expression of ZWF1 and optimize the timing of turning off the ZWF1, therefore, to determine the competitive equilibrium between glucose-xylose co-metabolism. This strategy allowed fast growth in the early stage of fermentation and low waste in the following stages of fermentation.

Enhancing xylose-fermentation capacity of engineered Saccharomyces cerevisiae by multistep evolutionary engineering in inhibitor-rich lignocellulose hydrolysate

Major progress in developing Saccharomyces cerevisiae strains that utilize the pentose sugar xylose has been achieved. However, the high inhibitor content of lignocellulose hydrolysates still hinders efficient xylose fermentation, which remains a major obstacle for commercially viable second-generation bioethanol production. Further improvement of xylose utilization in inhibitor-rich lignocellulose hydrolysates remains highly challenging. In this work, we have developed a robust industrial S. cerevisiae strain able to efficiently ferment xylose in concentrated undetoxified lignocellulose hydrolysates. This was accomplished with novel multistep evolutionary engineering. First, a tetraploid strain was generated and evolved in xylose-enriched pretreated spruce biomass. The best evolved strain was sporulated to obtain a genetically diverse diploid population. The diploid strains were then screened in industrially relevant conditions. The best performing strain, MDS130, showed superior fermentation performance in three different lignocellulose hydrolysates. In concentrated corncob hydrolysate, with initial cell density of 1 g DW/l, at 35°C, MDS130 completely coconsumed glucose and xylose, producing ± 7% v/v ethanol with a yield of 91% of the maximum theoretical value and an overall productivity of 1.22 g/l/h. MDS130 has been developed from previous industrial yeast strains without applying external mutagenesis, minimizing the risk of negative side-effects on other commercially important properties and maximizing its potential for industrial application.

Systematic genetic modifications of cell wall biosynthesis enhanced the secretion and surface-display of polysaccharide degrading enzymes in Saccharomyces cerevisiae

Saccharomyces cerevisiae is a robust cell factory to secrete or surface-display cellulase and amylase for the conversion of agricultural residues into valuable chemicals. Engineering the secretory pathway is a well-known strategy for overproducing these enzymes. Although cell wall biosynthesis can be tightly linked to the secretory pathway by regulation of all involved processes, the effect of its modifications on protein production has not been extensively studied. In this study, we systematically studied the effect of engineering cell wall biosynthesis on the activity of cellulolytic enzyme β-glucosidase (BGL1) by comparing seventy-nine gene knockout S. cerevisiae strains and newly identified that inactivation of DFG5, YPK1, FYV5, CCW12 and KRE1 obviously improved BGL1 secretion and surface-display. Combinatorial modifications of these genes, particularly double deletion of FVY5 and CCW12, along with the use of rich medium, increased the activity of secreted and surface-displayed BGL1 by 6.13-fold and 7.99-fold, respectively. Additionally, we applied this strategy to improve the activity of the cellulolytic cellobiohydrolase and amylolytic α-amylase. Through proteomic analysis coupled with reverse engineering, we found that in addition to the secretory pathway, regulation of translation processes may also involve in improving enzyme activity by engineering cell wall biosynthesis. Our work provides new insight into the construction of a yeast cell factory for efficient production of polysaccharide degrading enzymes.

Efficient biosynthesis of 3-hydroxypropionic acid from ethanol in metabolically engineered Escherichia coli

Engineering microbial cell factories to convert CO₂-based feedstock into chemicals and fuels provide a feasible carbon-neutral route for the third-generation biorefineries. Ethanol became one of the major products of syngas fermentation by engineered acetogens. The key building block chemical 3-hydroxypropionic acid (3-HP) can be synthesized from ethanol by the malonyl-CoA pathway with CO₂ fixation. In this study, the effect of two ethanol consumption pathways on 3-HP synthesis were studied as well as the effect of TCA cycle, gluconeogenesis pathway, and transhydrogenase. And the 3-HP synthesis pathway was also optimized. The engineered strain synthesized 1.66 g/L of 3-HP with a yield of 0.24 g/g. Furthermore, the titer and the yield of 3-HP increased to 13.17 g/L and 0.57 g/g in the whole-cell biocatalysis system. This study indicated that ethanol as feedstock had the potential to synthesize 3-HP, which provided an alternative route for future biorefinery.

Pretreatment Strategies to Enhance Enzymatic Hydrolysis and Cellulosic Ethanol Production for Biorefinery of Corn Stover

There is a rising interest in bioethanol production from lignocellulose such as corn stover to decrease the need for fossil fuels, but most research mainly focuses on how to improve ethanol yield and pays less attention to the biorefinery of corn stover. To realize the utilization of different components of corn stover in this study, different pretreatment strategies were used to fractionate corn stover while enhancing enzymatic digestibility and cellulosic ethanol production. It was found that the pretreatment process combining dilute acid (DA) and alkaline sodium sulfite (ASS) could effectively fractionate the three main components of corn stover, i.e., cellulose, hemicellulose, and lignin, that xylose recovery reached 93.0%, and that removal rate of lignin was 85.0%. After the joint pretreatment of DA and ASS, the conversion of cellulose at 72 h of enzymatic hydrolysis reached 85.4%, and ethanol concentration reached 48.5 g/L through fed-batch semi-simultaneous saccharification and fermentation (S-SSF) process when the final concentration of substrate was 18% (w/v). Pretreatment with ammonium sulfite resulted in 83.8% of lignin removal, and the conversion of cellulose and ethanol concentration reached 86.6% and 50 g/L after enzymatic hydrolysis of 72 h and fed-batch S-SSF, respectively. The results provided a reference for effectively separating hemicellulose and lignin from corn stover and producing cellulosic ethanol for the biorefinery of corn stover.

Production of cellulosic ethanol and value-added products from corn fiber

Corn fiber, a by-product from the corn processing industry, mainly composed of residual starch, cellulose, and hemicelluloses, is a promising raw material for producing cellulosic ethanol and value-added products due to its abundant reserves and low costs of collection and transportation. Now, several technologies for the production of cellulosic ethanol from corn fiber have been reported, such as the D3MAX process, Cellerate™ process, etc., and part of the technologies have also been used in industrial production in the United States. The ethanol yields range from 64 to 91% of the theoretical maximum, depending on different production processes. Because of the multicomponent of corn fiber and the complex structures highly substituted by a variety of side chains in hemicelluloses of corn fiber, however, there are many challenges in cellulosic ethanol production from corn fiber, such as the low conversion of hemicelluloses to fermentable sugars in enzymatic hydrolysis, high production of inhibitors during pretreatment, etc. Some technologies, including an effective pretreatment process for minimizing inhibitors production and maximizing fermentable sugars recovery, production of enzyme preparations with suitable protein compositions, and the engineering of microorganisms capable of fermenting hexose and pentose in hydrolysates and inhibitors tolerance, etc., need to be further developed. The process integration of cellulosic ethanol and value-added products also needs to be developed to improve the economic benefits of the whole process. This review summarizes the status and progresses of cellulosic ethanol production and potential value-added products from corn fiber and presents some challenges in this field at present.

Rapid evolution and mechanism elucidation for efficient cellobiose-utilizing Saccharomyces cerevisiae through Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution

Lack of cellobiose utilization capability for many microorganisms results in carbon source waste in lignocellulosic biorefinery. In this study, genes for cellobiose transport and hydrolysis were introduced to Saccharomyces cerevisiae synV, a semi-synthetic yeast with an inducible SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution) system incorporated into its chromosome V, endowing cellobiose utilization capability to this strain. Thereafter, two evolved strains with 98.1% and 79.2% improvement, respectively, in cellobiose utilization rate were obtained through induced SCRaMbLE. Further studies suggested that the enhanced cellobiose utilization capability directly correlated with copy number increases of introduced genes and some chromosome structural variations. In particular, it was experimentally demonstrated for the first time that deletion of redox stress related gene MXR1 and ATP conversion related gene ADK2 contributed to enhanced cellobiose conversion. Thereafter, the effectiveness of MXR1 and ADK2 deletions was demonstrated in artificial hydrolysate and rice straw hydrolysate, respectively.

Re-examination of dilute acid hydrolysis of lignocellulose for production of cellulosic ethanol after de-bottlenecking the inhibitor barrier

Dilute acid hydrolysis of lignocellulose biomass had been used for production of cellulosic ethanol since 1940s. The major technical barrier is the acid catalyzed dehydration of monosaccharides to furan aldehydes (furfural and 5-hydroxymethylfurfural), resulting in the high loss of fermentable sugars and significant inhibition on the fermentability of ethanologenic strains. This study re-examined the dilute acid hydrolysis of corn stover and cellulosic ethanol fermentation after a novel biodetoxification approach was introduced to de-bottleneck the inhibitor barrier. The cocktail of sulfuric acid, phosphoric acid and oxalic acid hydrolyzed corn stover to the 51.1g/L of glucose (0.50g/g cellulose) and 18.1g/L of xylose (0.22g/g xylan). The furfural, 5-hydroxymethylfurfural and acetic acid in the corn stover hydrolysate were completely removed by Paecilomyces variotii FN89, leading to the successful ethanol fermentation of 24.2g/L, corresponding to 72.6kg per metric ton of dry corn stover. No wastewater streams, solid wastes and toxic compounds were generated in hydrolysis, biodetoxification and fermentation. The techno-economic evaluations suggest that the cost reduction of replacing cellulase enzyme with cheap acid catalysts compensated the partial ethanol loss of sugar conversion to inhibitors (21.5-89.1%). The re-examination of acid hydrolysis process reveals that a substantial breakthrough in highly active and selective acid catalyst is required for acid hydrolysis to compete with enzymic hydrolysis for cellulosic ethanol fermentation.

Comparison of Spathaspora passalidarum and recombinant Saccharomyces cerevisiae for integration of first- and second-generation ethanol production

First-generation ethanol (E1G) is based on the fermentation of sugars released from saccharine or starch sources, while second-generation ethanol (E2G) is focused on the fermentation of sugars released from lignocellulosic feedstocks. During the fractionation process to release sugars from hemicelluloses (mainly xylose), some inhibitor compounds are released hindering fermentation. Thus, the biggest challenge of using hemicellulosic hydrolysate is selecting strains and processes able to efficiently ferment xylose and tolerate inhibitors. With the aim of diluting inhibitors, sugarcane molasses (80% of sucrose content) can be mixed to hemicellulosic hydrolysate in an integrated E1G-E2G process. Cofermentations of xylose and sucrose were evaluated for the native xylose consumer Spathaspora passalidarum and a recombinant Saccharomyces cerevisiae strain. The industrial S. cerevisiae strain CAT-1 was modified to overexpress the XYL1, XYL2 and XKS1 genes and a mutant ([4-59Δ]HXT1) version of the low-affinity HXT1 permease, generating strain MP-C5H1. Although S. passalidarum showed better results for xylose fermentation, this yeast showed intracellular sucrose hydrolysis and low sucrose consumption in microaerobic conditions. Recombinant S. cerevisiae showed the best performance for cofermentation, and a batch strategy at high cell density in bioreactor achieved unprecedented results of ethanol yield, titer and volumetric productivity in E1G-E2G production process.

Transformation of lignocellulose to starch-like carbohydrates by organic acid-catalyzed pretreatment and biological detoxification

Corn dry milling provides a mature model for lignocellulose biorefinery process. To copy this technical success, a crucial step is to transform lignocellulose into starch-like carbohydrates (SLC), similar to milled corn grain and in a similar fashion to corn dry milling. The transformation process should be zero wastewater generation and sufficient fermentable sugar conservation; the product should be in solid particle form, free of toxic residues, and high enzymatic hydrolysis yield and fermentability. Here we designed and verified a SLC transformation process by (i) biodegradable oxalic acid-catalyzed pretreatment, and (ii) simultaneous biodegradation of inhibitors and oxalic acid catalyst. The oxalic acid catalyst was effective on disrupting the lignocellulose structure and also biodegradable at low pH value. The biodetoxification fungus Paecilomyces variotii FN89 was capable of degrading the furan/phenolic aldehydes and oxalic acid simultaneously and ultimately, while the fermentable sugars were well preserved. The obtained SLC from wheat straw and corn stover were similar to dry milled corn meal in terms of morphological properties, fermentable sugar contents, enzymatic hydrolysis yield, elemental contents, and free of inhibitors and acid catalyst. The bioconversion of starch-like wheat straw and corn stover produced 78.5 and 75.3 g/L of ethanol (9.9% and 9.5%, v/v) with the yield of 0.47 and 0.45 g ethanol/g cellulose/xylose, respectively, compared with 78.7 g/L (10.0%, v/v) from corn meal and the yield of 0.48 g ethanol/g starch. Mass balances suggest that the ethanol yield, wastewater generation, and elemental recycling of the SLC from lignocellulose were essentially the same as those of corn meal.

Production of xylitol by Saccharomyces cerevisiae using waste xylose mother liquor and corncob residues

Exorbitant outputs of waste xylose mother liquor (WXML) and corncob residue from commercial‐scale production of xylitol create environmental problems. To reduce the wastes, a Saccharomyces cerevisiae strain tolerant to WXML was conferred with abilities to express the genes of xylose reductase, a xylose‐specific transporter and enzymes of the pentose phosphate pathway. This strain showed a high capacity to produce xylitol from xylose in WXML with glucose as a co‐substrate. Additionally, a simultaneous saccharification and fermentation (SSF) process was designed to use corncob residues and cellulase instead of directly adding glucose as a co‐substrate. Xylitol titer and the productivity were, respectively, 91.0 g l^‐1 and 1.26 ± 0.01 g l^‐1 h^‐1 using 20% WXML, 55 g DCW l^‐1 delignified corncob residues and 11.8 FPU g_cellulose^‐1 cellulase at 35° during fermentation. This work demonstrates the promising strategy of SSF to exploit waste products to xylitol fermentation process.

Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts

Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.

Formulating a fully converged biorefining chain with zero wastewater generation by recycling stillage liquid to dry acid pretreatment operation

Huge wastewater generation is the major challenge of biorefinery technology for production of cellulosic ethanol. This study designed and verified a method for completely recycling of wastewater stream (the stillage liquid from the beer column) in cellulosic ethanol production by dry biorefining processing. When the stillage liquid was directly recycled to dry acid pretreatment operation, ethanol production gradually reduced after two recycles primarily because the inorganic compounds accumulated by around 139%. To ultimately solve this technical barrier, the stillage liquid was evaporated and condensed into distillated water, then recycled to the pretreatment for complete dry biorefining process. This strategy supported a stable cellulosic ethanol production, and the overall mass and heat balance confirmed that only 65% of the lignin residue consumption was used for wastewater evaporation with 35% surplus for electricity generation. This study provided a fully converged biorefining process with a closed-loop wastewater recycling.

Sustainable environmental management and related biofuel technologies

Environmental sustainability criteria and rising energy demands, exhaustion of conventional resources of energy followed by environmental degradation due to abrupt climate changes have shifted the attention of scientists to seek renewable sources of green and clean energy for sustainable development. Bioenergy is an excellent alternative since it can be applied for several energy-requirements after utilizing suitable conversion methodology. This review elucidates all aspects of biofuels (bioethanol, biodiesel, and butanol) and their sustainability criteria. The principal focus is on the latest developments in biofuel production chiefly stressing on the role of nanotechnology. A plethora of investigations regarding the emerging techniques for process improvement like integration methods, less energy-intensive distillation techniques, and bioengineering of microorganisms are discussed. This can assist in making biofuel-production in a real-world market more economically and environmentally viable.

Increasing the level of 4-vinylguaiacol in top-fermented wheat beer by secretory expression of ferulic acid decarboxylase from Bacillus pumilus in brewer's yeast

OBJECTIVE

The objective is to explore the effects of enhancing the activity of yeast ferulic acid decarboxylase (FDC1) on the level of 4-vinylguaiacol (4-VG) and the consumption of its precursor ferulic acid (FA) in top-fermented wheat beer.

RESULTS

Expression of Bacillus pumilus FDC1 in brewer's yeast showed a better effect on the FDC1 activity than overexpression of the endogenous enzyme. The 4-VG content was increased by 34%, and the consumption time of FA was shortened from 48 to 12 h. Since the intracellular accumulation of the FDC1 substrate did not increase over time, to reduce the FA transport burden on cells and shorten the decarboxylation time, B. pumilus FDC1 was further secreted extracellularly. The resulted strain showed a 65% increase in 4-VG content in the FA-containing medium, and produced about 3 mg L^-1 4-VG in the top-fermented wheat beer, increasing by 61% than control. However, further increasing the secretory expression level of FDC1 only accelerated FA consumption.

CONCLUSIONS

These results suggested that appropriate secretion of bacterial FDC1 into wort could be used as a potential alternative strategy to increase the level of 4-VG in top-fermented wheat beer.

Improving Xylose Fermentation in Saccharomyces cerevisiae by Expressing Nuclear-Localized Hexokinase 2

Understanding the relationship between xylose and the metabolic regulatory systems is a prerequisite to enhance xylose utilization in recombinant S. cerevisiae strains. Hexokinase 2 (Hxk2p) is an intracellular glucose sensor that localizes to the cytoplasm or the nucleus depending on the carbon source. Hxk2p interacts with Mig1p to regulate gene transcription in the nucleus. Here, we investigated the effect of nucleus-localized Hxk2p and Mig1p on xylose fermentation. The results show that the expression of HXK2^S14A, which encodes a constitutively nucleus-localized Hxk2p, increased the xylose consumption rate, the ethanol production rate, and the ethanol yield of the engineered yeast strain by 23.5%, 78.6% and 42.6%, respectively. The deletion of MIG1 decreased xylose utilization and eliminated the positive effect of Hxk2p. We then performed RNA-seq and found that the targets of Hxk2p^S14A on xylose were mainly genes that encode RNA-binding proteins. This is very different from the known targets of Mig1p and supports the notion that the Hxk2p-Mig1p interaction is abolished in the presence of xylose. These results will improve our understanding of the interrelation between the Snf1p-Mig1p-Hxk2p glucose signaling pathway and xylose utilization in S. cerevisiae and suggests that the expression of HXK2^S14A could be a viable strategy to improve xylose utilization.

Identification and Characterization of an Efficient d-Xylose Transporter in Saccharomyces cerevisiae

d-Xylose is the most abundant hemicellulosic monomer on earth, but wild-type Saccharomyces cerevisiae has very limited d-xylose uptake capacity. We conducted bioprospecting for new sugar transporters from the d-xylose-consuming filamentous fungus Trichoderma reesei and identified three candidates belonging to the major facilitator superfamily. When they were expressed in yeast and assayed for d-xylose uptake, one of them, Xltr1p, had d-xylose transport activity that was more efficient than that of Gal2p, an endogenous yeast transporter. Site-directed mutagenesis was used to examine the functional contributions of 13 amino acid residues for the uptake of d-xylose, and these experiments identified particular amino acids that function distinctly in d-xylose vs glucose transport (e.g., F300). Excitingly, the yeast strain expressing the N326F^Xltr1p variant was able to carry a "high efficiency" transport for d-xylose but was nearly unable to utilize glucose; in contrast, the strain with the F300A^Xltr1p variant grew on glucose but lost d-xylose transport activity.

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.

Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome

Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.

Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains

p-Benzoquinone (BQ) is a lignin-derived inhibitor of biorefinery fermentation strains produced during pretreatment of lignocellulose. Unlike the well-studied inhibitors furan aldehydes, weak acids, and phenolics, the inhibitory properties of BQ, the microbial tolerance mechanism, and the detoxification strategy for this inhibitor have not been clearly elucidated. Here, BQ was identified as a by-product generated during acid pretreatment of various lignocellulose feedstocks, including corn stover, wheat straw, rice straw, tobacco stem, sunflower stem, and corncob residue. BQ at 20 to 200 mg/liter severely inhibited the cell growth and fermentability of various bacteria and yeast strains used in biorefinery fermentations. The BQ tolerance of the strains was found to be closely related to their capacity to convert BQ to nontoxic hydroquinone (HQ). To identify the key genes responsible for BQ tolerance, transcription levels of 20 genes potentially involved in the degradation of BQ in Zymomonas mobilis were investigated using real-time quantitative PCR in BQ-treated cells. One oxidoreductase gene, one hydroxylase gene, three reductase genes, and three dehydrogenase genes were found to be responsible for the conversion of BQ to HQ. Overexpression of the five key genes in Z. mobilis (ZMO1696, ZMO1949, ZMO1576, ZMO1984, and ZMO1399) accelerated its cell growth and cellulosic ethanol production in BQ-containing medium and lignocellulose hydrolysates.IMPORTANCE This study advances our understanding of BQ inhibition behavior and the mechanism of microbial tolerance to this inhibitor and identifies the key genes responsible for BQ detoxification. The insights here into BQ toxicity and tolerance provide the basis for future synthetic biology to engineer industrial fermentation strains with enhanced BQ tolerance.

Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha)

This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.

Microbial extraction of biotin from lignocellulose biomass and its application on glutamic acid production

Biotin (vitamin B₇) is an important nutrient for various fermentations. It is abundant in agricultural lignocellulose biomass and maintains stable in biorefinery processing chain including acid pretreatment, biodetoxification and saccharification. Here we show a microbial extraction of biotin from biotin-rich corn leaves hydrolysate. Corynebacterium glutamicum was found to have the highest biotin uptake capacity among different biotin auxotrophic microorganisms, and it was further significantly increased by overexpressing the bioYMN gene cluster encoding biotin transporter. Finally 250 folds greater biotin was extracted by recombinant C. glutamicum (303.8 mg/kg dry cell) from virgin corn leaves (1.2 mg/kg), which was far higher than that in commonly used fermentation additives including yeast extract (∼2 mg/kg), molasses (∼1 mg/kg) and corn steep liquor (∼0.75 mg/kg). The biotin extracted from corn leaves was successfully applied to glutamic acid fermentation. This is the first report on microbial extraction of biotin from lignocellulose biomass and fermentation promotion application.

A Thi2p Regulatory Network Controls the Post-glucose Effect of Xylose Utilization in Saccharomyces cerevisiae

The complete and efficient utilization of both glucose and xylose is necessary for the economically viable production of biofuels and chemicals using lignocellulosic feedstocks. Although recently obtained recombinant Saccharomyces cerevisiae strains metabolize xylose well when xylose is the sole carbon source in the medium (henceforth referred to as "X stage"), their xylose consumption rate is significantly reduced during the xylose-only consumption phase of glucose-xylose co-fermentation ("GX stage"). This post-glucose effect seriously decreases overall fermentation efficiency. We showed in previous work that THI2 deletion can alleviate this post-glucose effect, but the underlying mechanisms were ill-defined. In the present study, we profiled the transcriptome of a thi2Δ strain growing at the GX stage. Thi2p in GX stage cells regulates genes involved in the cell cycle, stress tolerance, and cell viability. Importantly, the regulation of Thi2p differs from a previous regulatory network that functions when glucose is the sole carbon source, which suggests that the function of Thi2p depends on the carbon source. Modeling research seeking to optimize metabolic engineering via TFs should account for this important carbon source difference. Building on our initial study, we confirmed that several identified factors did indeed increase fermentation efficiency. Specifically, overexpressing STT4, RGI2, and TFC3 increases specific xylose utilization rate of the strain by 36.9, 29.7, 42.8%, respectively, in the GX stage of anaerobic fermentation. Our study thus illustrates a promising strategy for the rational engineering of yeast for lignocellulosic ethanol production.

Enhanced ethanol production from industrial lignocellulose hydrolysates by a hydrolysate-cofermenting Saccharomyces cerevisiae strain

Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a hydrolysate-cofermenting Saccharomyces cerevisiae strain was obtained through one step in vivo DNA assembly of pentose-metabolizing pathway genes, followed by consecutive adaptive evolution in pentose media containing acetic acid, and direct screening in biomass hydrolysate media. The strain was able to coferment glucose and xylose in synthetic media with the respective maximal specific rates of glucose and xylose consumption, and ethanol production of 3.47, 0.38 and 1.62 g/g DW/h, with an ethanol titre of 41.07 g/L and yield of 0.42 g/g. Industrial wheat straw hydrolysate fermentation resulted in maximal specific rates of glucose and xylose consumption, and ethanol production of 2.61, 0.54 and 1.38 g/g DW/h, respectively, with an ethanol titre of 54.11 g/L and yield of 0.44 g/g. These are among the best for wheat straw hydrolysate fermentation through separate hydrolysis and cofermentation.

Cow manure as a lignocellulosic substrate for fungal cellulase expression and bioethanol production

Conversion of various lignocellulosic materials into bioethanol is growing in demand but greatly depends on feedstock availability. Dairy cow manure is an agricultural waste widely distributed worldwide. This study investigated the induction of cellulases by cow manure and the conversion of cow manure materials into lignocellulosic ethanol. Alkaline NaOH pretreatment improved the accessibility of cow manure lignocellulose to enzymes followed by enzymatic hydrolysis using Penicillium oxalicum cellulases. The ethanol yields from pretreated cow manure and anaerobically digested cow manure were 0.19 and 0.13 g/g-raw biomass, respectively, using recombinant Saccharomyces cerevisiae strain LF1 designed for lignocellulosic ethanol production through simultaneous saccharification and fermentation. Fed-batch supplementation with cellulolytic enzymes and substrates after initial enzymatic hydrolysis also contributed to ethanol production up to 25.65 g/L. These results demonstrate that cow manure is a potential feedstock for inducing fungal cellulase expression and converting lignocellulose into bioethanol.

Augmenting Pentose Utilization and Ethanol Production of Native Saccharomyces cerevisiae LN Using Medium Engineering and Response Surface Methodology

Economics of ethanol production from lignocellulosic biomass depends on complete utilization of constituent carbohydrates and efficient fermentation of mixed sugars present in biomass hydrolysates. Saccharomyces cerevisiae, the commercial strain for ethanol production uses only glucose while pentoses remain unused. Recombinant strains capable of utilizing pentoses have been engineered but with limited success. Recently, presence of endogenous pentose assimilation pathway in S. cerevisiae was reported. On the contrary, evolutionary engineering of native xylose assimilating strains is promising approach. In this study, a native strain S. cerevisiae LN, isolated from fruit juice, was found to be capable of xylose assimilation and mixed sugar fermentation. Upon supplementation with yeast extract and peptone, glucose (10%) fermentation efficiency was 78% with ~90% sugar consumption. Medium engineering augmented mixed sugars (5% glucose + 5% xylose) fermentation efficiency to ~50 and 1.6% ethanol yield was obtained with concomitant sugar consumption ~60%. Statistical optimization of input variables Glucose (5.36%), Xylose (3.30%), YE (0.36%), and peptone (0.25%) with Response surface methodology led to improved sugar consumption (74.33%) and 2.36% ethanol within 84 h. Specific activities of Xylose Reductase and Xylitol Dehydrogenase exhibited by S. cerevisiae LN were relatively low. Their ratio indicated metabolism diverted toward ethanol than xylitol and other byproducts. Strain was tolerant to concentrations of HMF, furfural and acetic acid commonly encountered in biomass hydrolysates. Thus, genetic setup for xylose assimilation in S. cerevisiae LN is not merely artifact of xylose metabolizing pathway and can be augmented by adaptive evolution. This strain showed potential for commercial exploitation.

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.

Ethanol production potential from AFEX™ and steam-exploded sugarcane residues for sugarcane biorefineries

BACKGROUND

Expanding biofuel markets are challenged by the need to meet future biofuel demands and mitigate greenhouse gas emissions, while using domestically available feedstock sustainably. In the context of the sugar industry, exploiting under-utilized cane leaf matter (CLM) in addition to surplus sugarcane bagasse as supplementary feedstock for second-generation ethanol production has the potential to improve bioenergy yields per unit land. In this study, the ethanol yields and processing bottlenecks of ammonia fibre expansion (AFEX™) and steam explosion (StEx) as adopted technologies for pretreating sugarcane bagasse and CLM were experimentally measured and compared for the first time.

RESULTS

Ethanol yields between 249 and 256 kg Mg-1 raw dry biomass (RDM) were obtained with AFEX™-pretreated sugarcane bagasse and CLM after high solids loading enzymatic hydrolysis and fermentation. In contrast, StEx-pretreated sugarcane bagasse and CLM resulted in substantially lower ethanol yields that ranged between 162 and 203 kg Mg-1 RDM. The ethanol yields from StEx-treated sugarcane residues were limited by the aggregated effect of sugar degradation during pretreatment, enzyme inhibition during enzymatic hydrolysis and microbial inhibition of S. cerevisiae 424A (LNH-ST) during fermentation. However, relatively high enzyme dosages (> 20 mg g-1 glucan) were required irrespective of pretreatment method to reach 75% carbohydrate conversion, even when optimal combinations of Cellic® CTec3, Cellic® HTec3 and Pectinex Ultra-SP were used. Ethanol yields per hectare sugarcane cultivation area were estimated at 4496 and 3416 L ha-1 for biorefineries using AFEX™- or StEx-treated sugarcane residues, respectively.

CONCLUSIONS

AFEX™ proved to be a more effective pretreatment method for sugarcane residues relative to StEx due to the higher fermentable sugar recovery and enzymatic hydrolysate fermentability after high solids loading enzymatic hydrolysis and fermentation by S. cerevisiae 424A (LNH-ST). The identification of auxiliary enzyme activities, adequate process integration and the use of robust xylose-fermenting ethanologens were identified as opportunities to further improve ethanol yields from AFEX™- and StEx-treated sugarcane residues.

Disruption of the transcription factors Thi2p and Nrm1p alleviates the post-glucose effect on xylose utilization in Saccharomyces cerevisiae

BACKGROUND

The recombinant Saccharomyces cerevisiae strains that acquired the ability to utilize xylose through metabolic and evolutionary engineering exhibit good performance when xylose is the sole carbon source in the medium (designated the X stage in the present work). However, the xylose consumption rate of strains is generally low after glucose depletion during glucose-xylose co-fermentation, despite the presence of xylose in the medium (designated the GX stage in the present work). Glucose fermentation appears to reduce the capacity of these strains to "recognize" xylose during the GX stage, a phenomenon termed the post-glucose effect on xylose metabolism.

RESULTS

Two independent xylose-fermenting S. cerevisiae strains derived from a haploid laboratory strain and a diploid industrial strain were used in the present study. Their common characteristics were investigated to reveal the mechanism underlying the post-glucose effect and to develop methods to alleviate this effect. Both strains showed lower growth and specific xylose consumption rates during the GX stage than during the X stage. Glycolysis, the pentose phosphate pathway, and translation-related gene expression were reduced; meanwhile, genes in the tricarboxylic acid cycle and glyoxylic acid cycle demonstrated higher expression during the GX stage than during the X stage. The effects of 11 transcription factors (TFs) whose expression levels significantly differed between the GX and X stages in both strains were investigated. Knockout of THI2 promoted ribosome synthesis, and the growth rate, specific xylose utilization rate, and specific ethanol production rate of the strain increased by 17.4, 26.8, and 32.4%, respectively, in the GX stage. Overexpression of the ribosome-related genes RPL9A, RPL7B, and RPL7A also enhanced xylose utilization in a corresponding manner. Furthermore, the overexpression of NRM1, which is related to the cell cycle, increased the growth rate by 8.7%, the xylose utilization rate by 30.0%, and the ethanol production rate by 76.6%.

CONCLUSIONS

The TFs Thi2p and Nrm1p exerted unexpected effects on the post-glucose effect, enhancing ribosome synthesis and altering the cell cycle, respectively. The results of this study will aid in maintaining highly efficient xylose metabolism during glucose-xylose co-fermentation, which is utilized for lignocellulosic bioethanol production.

Biocontrol ability of killer yeasts (Saccharomyces cerevisiae) isolated from wine against Colletotrichum gloeosporioides on grape

A total of 216 killer yeasts Saccharomyces cerevisiae, isolated from wine, were evaluated in controlling Colletotrichum gloeosporioides, a pre-harvest anthracnose agent of grape. Three of these yeast isolates were tested positive for antagonizing C. gloeosporioides and were further evaluated for their mechanisms as biological control agents (BCAs): production of antifungal compounds, production of hydrolytic enzymes, inhibition of C. gloeosporioides conidia germination, colonization on grape berry, and efficiency in controlling anthracnose of grape. The results showed that all three S. cerevisiae isolates produced antifungal compounds, inhibited C. gloeosporioides conidia germination and produced β-1,3-glucanase and chitinase. All isolates colonized grape berry in large quantities and controlled C. gloeosporioides when artificially inoculated on grape berry. Among the three isolates, application of isolate GA8 resulted in 69.7% of disease reductions for C. gloeosporioides on grape berry. The antagonistic isolates of S. cerevisiae could represent important BCAs of anthracnose of grape caused by C. gloeosporioides that are responsible for economic losses in viticulture.

Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation

The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.

Screening and characterizing of xylanolytic and xylose-fermenting yeasts isolated from the wood-feeding termite, Reticulitermes chinensis

The effective fermentation of xylose remains an intractable challenge in bioethanol industry. The relevant xylanase enzyme is also in a high demand from industry for several biotechnological applications that inevitably in recent times led to many efforts for screening some novel microorganisms for better xylanase production and fermentation performance. Recently, it seems that wood-feeding termites can truly be considered as highly efficient natural bioreactors. The highly specialized gut systems of such insects are not yet fully realized, particularly, in xylose fermentation and xylanase production to advance industrial bioethanol technology as well as industrial applications of xylanases. A total of 92 strains from 18 yeast species were successfully isolated and identified from the gut of wood-feeding termite, Reticulitermes chinensis. Of these yeasts and strains, seven were identified for new species: Candida gotoi, Candida pseudorhagii, Hamamotoa lignophila, Meyerozyma guilliermondii, Sugiyamaella sp.1, Sugiyamaella sp. 2, and Sugiyamaella sp.3. Based on the phylogenetic and phenotypic characterization, the type strain of C. pseudorhagii sp. nov., which was originally designated strain SSA-1542^T, was the most frequently occurred yeast from termite gut samples, showed the highly xylanolytic activity as well as D-xylose fermentation. The highest xylanase activity was recorded as 1.73 and 0.98 U/mL with xylan or D-xylose substrate, respectively, from SSA-1542^T. Among xylanase-producing yeasts, four novel species were identified as D-xylose-fermenting yeasts, where the yeast, C. pseudorhagii SSA-1542^T, showed the highest ethanol yield (0.31 g/g), ethanol productivity (0.31 g/L·h), and its fermentation efficiency (60.7%) in 48 h. Clearly, the symbiotic yeasts isolated from termite guts have demonstrated a competitive capability to produce xylanase and ferment xylose, suggesting that the wood-feeding termite gut is a promising reservoir for novel xylanases-producing and xylose-fermenting yeasts that are potentially valued for biorefinery industry.