Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering
- Mekonnen M Demeke†1, 2,
- Heiko Dietz†3,
- Yingying Li1, 2,
- María R Foulquié-Moreno1, 2,
- Sarma Mutturi4,
- Sylvie Deprez5,
- Tom Den Abt1, 2,
- Beatriz M Bonini1, 2,
- Gunnar Liden4,
- Françoise Dumortier1, 2,
- Alex Verplaetse5,
- Eckhard Boles3 and
- Johan M Thevelein1, 2Email author
© Demeke et al.; licensee BioMed Central Ltd. 2013
Received: 6 March 2013
Accepted: 12 June 2013
Published: 21 June 2013
The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production.
An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate.
An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates.
KeywordsBioethanol Lignocellulose D-xylose fermentation D-xylose isomerase Inhibitor tolerance Saccharomyces cerevisiae Evolutionary engineering
The yeast Saccharomyces cerevisiae is still the dominant organism for industrial bioethanol production owing to its high rate of fermentation of hexose sugars, high tolerance to ethanol, inhibitors, acidity and other industrial process conditions, well-established production, storage and transport systems at commercial scale, comprehensive physiological and molecular knowledge and its genetic tractability [1, 2]. Unfortunately, baker’s yeast is unable to efficiently metabolize pentose sugars, particularly D-xylose, which accounts for up to 35% of total sugars in xylan-rich lignocellulosic biomass such as hard woods and straw . Although there are various species of bacteria, filamentous fungi and other yeast species that are naturally capable of efficiently metabolizing D-xylose, they lack the other crucial advantages of the yeast S. cerevisiae, which have made it the most prominent industrial microorganism. Lignocellulose hydrolysates contain various inhibitors depending on the type of biomass and pretreatment methodology used, making extreme inhibitor tolerance a crucial trait for reaching economically viable second-generation bioethanol production [4, 5]. The inherently higher robustness and tolerance of S. cerevisiae to various inhibitors gives it a head start in programs aimed at developing strains with extreme inhibitor tolerance, able to efficiently ferment hexoses and pentoses in concentrated lignocellulose hydrolysates . Although progress has been made in developing strains with higher ethanol and inhibitor tolerance in bacteria, like Escherichia coli, and in other yeast species, like Scheffersomyces (Pichia) stipitis, these strains still lag far behind industrial S. cerevisiae strains in their level of ethanol tolerance, general robustness and performance under industrial conditions [7, 8].
The engineering of novel metabolic capacities into robust microorganisms may be easier than the alternative strategy, i.e. engineering of very high ethanol tolerance and prominent general robustness. Impressive progress has been made in engineering pentose fermentation capacity into the yeast S. cerevisiae[9, 10]. For that purpose, two heterologous pathways for D-xylose utilization have been utilized. First, the genes encoding D-xylose reductase (XR) and xylitol dehydrogenase (XDH) from Scheffersomyces (Pichia) stipitis have been expressed in S. cerevisiae. This resulted in D-xylose fermentation, but also in significant production of xylitol under anaerobic conditions, which is due to NADH/NADPH cofactor imbalance of XR and XDH . The performance of these strains has been improved considerably by addressing the cofactor imbalance and by over-expression of endogenous xylulokinase (XK) and enzymes of the non-oxidative part of the pentose phosphate pathway [12–17].
The second pathway allows direct isomerization of D-xylose to xylulose through heterologous expression of xylose isomerase (XI). After the first successful attempt to express the thermophilic bacterium Thermus thermophilus XI into S. cerevisiae , recombinant strains expressing the fungal Piromyces sp. strain E2 xylose isomerase have been reported with better enzymatic activity [19, 20]. By using an isomerization instead of a reduction/oxidation conversion of D-xylose to xylulose, the problem of co-factor imbalance is avoided. However, the rate of D-xylose utilization in XI expressing strains was found to be inferior to that in strains harboring the XR/XDH pathway . This was mostly attributed to the low activity of the XI enzyme in S. cerevisiae and its inhibition by xylitol, generated from reduction of D-xylose by the endogenous enzymes encoded by GRE3, GCY1, YPR1, YDL124W and YJR096W [22–24]. The level of xylitol produced is much lower, however, than in the strains expressing the XR/XDH pathway. Deletion of GRE3 in an XI expressing strain improved both the rate of D-xylose consumption and ethanol production . The aldose reductase, encoded by GRE3, plays a role in stress protection and its deletion is therefore not desirable in industrial yeast strains . To overcome these problems, Brat et al.,  constructed the first recombinant S. cerevisiae strain demonstrating high activity of prokaryotic XI, using codon-optimized XylA gene from Clostridium phytofermentans. This enzyme was much less inhibited by xylitol compared to the enzyme from Piromyces. Nevertheless, the rate of D-xylose consumption and ethanol production by this recombinant strain was still slow.
Different metabolic and evolutionary engineering strategies have been used successfully to improve D-xylose utilization in a yeast strain expressing Piromyces xylose isomerase. Overexpression of genes encoding xylulokinase and enzymes of the non-oxidative part of the pentose phosphate pathway, combined with deletion of GRE3 to reduce xylitol formation, considerably improved the D-xylose consumption rate . This finally resulted in strains with strong pentose fermentation capacity and partial cofermentation of glucose and D-xylose [28, 29]. Moreover, the xylose isomerase pathway was compatible with the bacterial L-arabinose utilization pathway, in contrast to the XR/XDH pathway . These results suggested that the xylose isomerase pathway might be the pathway of choice for constructing superior industrial yeast strains with optimal fermentation performance in lignocellulose hydrolysates . However, all these engineered strains were still made in a haploid laboratory yeast strain background, displaying in general suboptimal fermentation performance and poor robustness and stress tolerance, which makes them unsuitable for use in industrial fermentations. Since previous work showed that XI expressing strains displayed higher yield of ethanol per consumed D-xylose compared to strains harboring the XR/XDH pathway  and since they profit from direct isomerization of D-xylose to xylulose without cofactor requirement, the XI pathway seemed to be most promising to engineer into a robust industrial yeast strain.
In this work, we have selected Ethanol Red as industrial host strain to engineer high-capacity pentose-fermentation, because it is one of the most widely used yeast strains for first-generation bioethanol production. The strain has excellent fermentation capacity, high robustness and stress tolerance, and also displays excellent performance in fed-batch production on molasses, is tolerant to dehydration and retains high vitality during storage and transport. Using this strain, we have developed the first industrial S. cerevisiae strain that converts D-xylose to ethanol with a yield close to the theoretical maximum yield and with a very high specific rate of fermentation. For that purpose, a recombinant strain was first constructed by chromosomal integration of codon-optimized XylA from C. phytofermentans in an over-expression gene cassette containing genes of the non-oxidative pentose phosphate pathway and the D-xylose transporting hexose transporter HXT7. Subsequently, we have used Ethyl Methanesulfonate (EMS) mutagenesis, genome shuffling and selection in lignocellulose hydrolysate, enriched with D-xylose, and subsequent evolutionary adaptation in complex medium with D-xylose, to greatly enhance both D-xylose utilization efficiency and inhibitor tolerance. The activity of XI was dramatically increased in the evolved strain, but other genetic changes were also required for its superior D-xylose fermentation capacity in lignocellulose hydrolysates.
Insertion of D-xylose utilization cassette into the Ethanol Red strain
The sporulation efficiency of the seven mutant strains was evaluated prior to the genome shuffling step. Only one of the mutant strains, M492, was still able to sporulate. The 3 to 4 h EMS treatment possibly caused mutations abolishing sporulation capacity in the other strains. The best D-xylose utilizing mutant strain M315 had MAT α mating type and was shown to be diploid by flow cytometry, indicating that the strain was a MAT α/α diploid. The M315 mutant was able to mate with MATa cells and we then used the two mutant strains, M315 and M492, together with the parent strain HDY.GUF5 for the genome shuffling step. The parent strain was included to facilitate loss of deleterious mutations.
The M492 mutant strain and the parent strain HDY.GUF5 were sporulated to more than 75% efficiency and the spores were liberated by zymolyase treatment. The mass of isolated spores from the two strains was allowed to germinate in YPD and then mass-mated with exponentially growing cells of the mutant M315. The zygotes from the mass mating were subsequently allowed to proliferate at 35°C in synthetic medium containing D-xylose as sole carbon source. The OD600 increased from 2.5 to 12 in 24 h. The whole cell population was then transferred into undetoxified spruce hydrolysate, supplemented with YP and 40 g/L D-xylose. The concentration of spruce hydrolysate used prevented growth of the parent strain HDY.GUF5, but the shuffled culture was able to grow in 48 h from an initial OD600 of 2 to an OD600 of 26. Acid pre-treated spruce hydrolysate supplemented with 40 g/L D-xylose was chosen for selection, because it contains a high amount of inhibitors and only a limited amount of D-glucose (13 g/L). When the glucose was used up, the strains continued to grow on the supplemented D-xylose, allowing us to select inhibitor tolerant mutants without losing the capacity to grow on D-xylose.
Eventually, the isolated spores from M492 and HDY.GUF5 were evaluated individually for spore viability by spreading the isolated spores on YPD plates. While none of the spores from M492 tested were viable, the expected number of cells (about 103) were germinated from the parent HDY.GUF5, indicating that mainly the HDY.GUF5 and the mutant M315 were involved in the genome shuffling step, while the M492 strain likely had a much lower or no contribution at all.
In order to enrich for fast D-xylose utilizing clones and subsequently improve the D-xylose utilization rate, the entire population of cells obtained after genome shuffling and subsequent selection in spruce hydrolysate with D-xylose, was used for the evolutionary engineering process. The cells were first grown aerobically in shake flasks containing 40 ml YPX medium for 48 h and then used for inoculation at an initial OD600 of 2.75 into cylindrical 150 ml fermentation tubes containing 100 ml YP medium with 40 g/L D-xylose. The fermentations were performed at 35°C under semi-anaerobic conditions, which were attained by slow stirring of the culture at 120 rpm to insure mixing of the cells without significant aeration. This method gradually created semi-anaerobic conditions (oxygen level of less than 1 ppm) within 1 h of incubation. The fermentation rate of the first culture, called GS1.1 was slow but already much better compared to the original strains used in the genome shuffling (Figure 2a). We then performed ten additional serial transfers using the same medium, each time with an initial cell density with OD600 of 5 (equivalent to 1.3 g DW/L). A relatively high inoculation density was used to insure that new variants of the cell population that were generated during the evolutionary process were effectively transferred to the next batch. In addition, complex medium, rather than defined mineral medium, was chosen for cultivation to avoid selective pressure due to nutrient limitation. As a result, the D-xylose utilization rate was the main selective criterion.
In the second culture, GS1.2, the lag phase was much longer than in the first culture, GS1.1, probably due to loss of viability during the prolonged incubation of the GS1.1 culture. However, a sharp rise in D-xylose consumption rate, as indicated by the CO2 production rate, was observed after 112 h (Figure 2a). To avoid possible loss of viability because of substrate depletion, subsequent serial transfers were performed each time before complete D-xylose depletion. Considerable improvement in the rate of D-xylose consumption was observed with each round of evolutionary adaptation (Figure 2a). The most dramatic change happened in the 3rd culture, GS1.3, in which almost no lag phase was observed, as opposed to the 112 h lag phase in the previous GS1.2 culture. In the 8th, 9th and 10th culture, the concentration of D-xylose was increased to 50 g/L, 60 g/L and 100 g/L, respectively, to further adapt the yeast to higher D-xylose concentrations with the assumption that higher concentrations of D-xylose might increase the rate of fermentation due to higher flux through the pathway. For the last culture, GS1.11, 40 g/L D-xylose was used again to make sure that the strain could also utilize lower D-xylose concentrations at a similar rate.
The progress of the evolutionary engineering process was continuously monitored by evaluation of single cell clones. A total of 9, 15, 20 and 27 single cell isolates from the 2nd, 4th, 7th and 11th culture, respectively, that were able to grow well on YPX plates, were evaluated for fermentation performance in YP + 40 g/L D-xylose (Figure 2b). A previously constructed industrial D-xylose utilizing stain, TMB3400, expressing xylose reductase and xylitol dehydrogenase , and the parent strain HDY.GUF5, were included for comparison (Figure 2b). Some isolates from the 2nd and 4th culture were already better than TMB3400 in terms of D-xylose fermentation rate (Figure 2b). However, all isolates from the 7th and 11th culture showed a much faster rate and much higher extent of D-xylose utilization than TMB3400 (Figure 2b). The individual clones isolated from the 7th and 11th culture showed a similar rate and extent of fermentation and therefore the evolutionary adaptation process was terminated after the 11th culture.
Selection of the best D-xylose fermenting strain
Fermentation performance of strain GS1.11-26 with D-xylose and a glucose/D-xylose mixture
In synthetic medium with 35 g/L D-xylose as sole carbon source, the evolved strain consumed all the available D-xylose in about 17 h, (Figure 5a) with maximum D-xylose consumption rate of 1.10 g/g DW/h and maximum ethanol production rate of 0.48 g/g DW/h. The final yield of ethanol was 0.46 g/g D-xylose and the xylitol yield was less than 0.01 g/g D-xylose. Though yeast strains expressing XI produce less xylitol compared to those of XR/XDH expressing strains , the presence of other enzymes such as the non-specific aldose reductase encoded by GRE3 results in conversion of D-xylose to xylitol . Since the xylitol yield in the strain GS1.11-26 was very low, we sequenced the GRE3 gene in both the parent and the final evolved strain to test for possible mutations abolishing its function. However, the sequences were found to be identical in both strains.
Comparison of fermentation performance between the parent strain, HDY.GUF5, and the evolved strain, GS1.11-26, in YP medium containing a glucose and D-xylose mixture
Maximum specific sugar consumption rate
Specific ethanol productivity
3.83 ± 0.08
0.13 ± 0.01
0.23 ± 0.00
0.03 ± 0.00
0.04 ± 0.00
1.79 ± 0.08
2.71 ± 0.04
1.10 ± 0.00
0.46 ± 0.00
0.04 ± 0.00
0.06 ± 0.00
1.38 ± 0.01
Fermentation performance of strain GS1.11-26 in lignocellulose hydrolysates
Separate hydrolysis and fermentation (SHF)
Composition of the three lignocellulose hydrolysates and fermentation yield of the evolved strain, GS1.11-26
Initial sugar level
Initial inhibitor concentration (g/L)
0.47 ± 0.01
0.07 ± 0.00
0.04 ± 0.00
0.43 ± 0.00
0.003 ± 0.000
0.04 ± 0.00
0.48 ± 0.02
0.04 ± 0.00
Arundo donax hydrolysate contained the highest acetate concentration from the three hydrolysates tested. An acetate concentration of about 4 g/L at low pH is known to be inhibitory to growth and fermentation of yeast [39, 40]. Moreover, D-xylose fermentation is more sensitive to acetate [41, 42]. Despite the presence of an initial acetate concentration of 6.8 g/L in the Arundo donax hydrolysate used, the strain consumed all the glucose and more than 90% of the D-xylose in about 96 h with an ethanol yield of 0.47 g/g total sugar, equivalent to 92% of the maximum theoretical ethanol yield (Figure 6a) (Table 2). A final ethanol titer of 4.1% (v/v) was reached in 96 h.
The D-xylose consumption rate was slower in spruce hydrolysate, possibly due to the high concentration of 5-hydroxymethyl-2-furaldehyde (HMF) and furfural in addition to the high acetate level. The initial level of D-xylose was lower than in the other two hydrolysates (Figure 6b), (Table 2). Acid pretreated spruce has been reported to be among the most-inhibitory hydrolysates. It contains high concentrations of phenolic compounds, weak acids and furan derivatives, that synergistically inhibit yeast growth and fermentation [8, 43]. Although we measured only the furans and acetic acid, the concentration of these compounds, especially HMF and furfural, was much higher in spruce than in the other two hydrolysates. Furfural and HMF were completely consumed in 4 h, while acetate remained in the medium. In spite of the elevated inhibitor concentrations, a high ethanol yield of 0.43 g/g initial soluble sugars was produced. This is remarkable in view of the high inhibitor concentration.
The wheat straw/hay hydrolysate contained the highest initial sugar concentration and the lowest level of inhibitors (Table 2). Both glucose and D-xylose were completely consumed in about 24 h producing a final ethanol concentration of 45.07 ± 0.92 g/L (Figure 6c), equivalent to 5.8% (v/v). This was the highest ethanol concentration of all three hydrolysates. The rapid fermentation and complete sugar attenuation in wheat straw/hay hydrolysate is likely due to the low level of inhibitors (Table 2).
Simultaneous saccharification and fermentation (SSF)
Final sugar and metabolite concentrations measured after 96 h SSF with the strain GS1.11-26 using steam pretreated spruce
Residual glucose (g/L)
Residual xylose (g/L)
Final ethanol concentration
Yield (g ethanol/g total sugar)*
% of maximum yield
Performance of strain GS1.11-26 in high-density fermentation
Growth rate of strain GS1.11-26 under aerobic conditions
The production of a maximal amount of yeast cell biomass under aerobic conditions is one of the requirements for industrial yeast propagation. The latter is performed in highly-controlled aerobic fed-batch fermentation in which the sugar level is maintained at a very low level (below 0.1% w/v) to avoid any production of ethanol. Hence, the yeast should be able to combine a high growth rate with a purely respiratory metabolism to maximize the production of biomass . With this notion, the strain GS1.11-26 was evaluated for growth rate under aerobic conditions in different media and volumes. In a bioscreen assay with synthetic medium containing 20 g/L glucose, the maximum respiro-fermentative growth rate of the evolved strain, GS1.11-26, was only about 75% (0.342 ± 0.005 h-1) of that of the parent strain, HDY.GUF5, (0.459 ± 0.021 h-1). Moreover, the mutants M315 and M492, which were used for the genome shuffling step, grew faster than GS1.11-26 and slower than HDY.GUF5. This might indicate that the genetic changes causing the slower aerobic growth rate in GS1.11-26 occurred both during mutagenesis and the subsequent genome shuffling and/or evolutionary adaptation process.
Stability of the D-xylose fermentation phenotype in strain GS1.11-26
Enhanced D-xylose isomerase activity in strain GS1.11-26
The very strong increase in XI activity might be a major reason for the improved D-xylose fermentation rate in the GS1.11-26 strain. The final XI specific activity of 0.57 U/mg protein is in the same range as previously reported values for evolutionary engineered strains expressing fungal Piromyces XI [50, 51]. The M315 mutant, selected after the mutagenesis procedure, did not show any increase in XI activity compared to the parent strain HDY.GUF5 (Figure 14a).
To assess the importance of the enhanced XI activity, we overexpressed the original Clostridium phytofermentans XylA gene construct on a multi-copy plasmid in the parent strain, HDY.GUF5, and the M315 mutant selected after the mutagenesis procedure. There was no improvement in the D-xylose fermentation rate in transformants of HDY.GUF5 (Figure 14b). On the other hand, the M315 mutant with the XylA overexpression plasmid showed a strong improvement in the D-xylose fermentation rate, although the rate was still much lower than that of the final evolved strain, GS1.11-26 (Figure 14b). This indicates that high XI activity is indeed beneficial for D-xylose fermentation but that it requires one or more mutations in the genome of the strain, which were introduced during the mutagenesis procedure, to be effective. In strain GS1.11-26 additional overexpression of XylA did not result in further improvement in the D-xylose fermentation rate, indicating that XI activity is no longer limiting the fermentation in this evolved strain under the experimental conditions used.
The XI from C. phytofermentans was the first prokaryotic XI that showed high activity upon expression in Saccharomyces cerevisiae, both in laboratory and industrial strains . However, the industrial strain expressing the codon-optimized version of the gene could only ferment D-xylose to ethanol after further evolutionary adaptation in D-xylose medium. Though the rate of D-xylose utilization by the evolved strain was much too low to allow industrially viable ethanol production from lignocellulosic feedstocks, the work provided a starting point for the development of strains using a bacterial XI that was less inhibited by xylitol than the fungal Piromyces XI. In the present work we combined rational metabolic engineering based on expression of the C. phytofermentans XI with systematic evolutionary engineering, and developed a robust industrial S. cerevisiae strain that efficiently converts D-xylose to ethanol with high yield and productivity.
Rational metabolic engineering alone was not able to establish efficient D-xylose (or L-arabinose) utilization capacity in the Ethanol Red strain. The recombinant strain HDY.GUF5 failed to show significant D-xylose (or L-arabinose) fermentation. Efficient rational engineering strategies rely on the complete understanding of the metabolic network, as well as its regulation in response to the dynamic environmental conditions to which the engineered strain is exposed . Because of the complexity and still limited understanding of the biological and regulatory network of D-xylose metabolism in recombinant S. cerevisiae strains, rational approaches have faced huge challenges to eliminate the factors that limit efficient D-xylose fermentation . Several of these factors have been identified [31, 52]. Most of these requirements have been addressed in the strain HDY.GUF5, which include overexpression of the PPP genes, XKS1 and the hexose/pentose transporter encoding gene HXT7, as well as codon optimization of some of the genes based on the highly efficient glycolytic codon usage of yeast . Although expression of the same codon-optimized XI in a laboratory strain established moderate D-xylose fermentation , the industrial strain used in this study as well as previously , was not able to metabolize D-xylose. This is likely due to the difference in the genetic background of the strains, although the precise mechanism remains unclear .
Combining metabolic engineering with evolutionary engineering alone or together with random mutagenesis has been proven successful for developing strains with improved D-xylose fermentation efficiency [20, 29, 51, 54, 55]. In addition, genome shuffling has also been used in combination with metabolic engineering and evolutionary adaptation, for improving D-xylose utilization capacity in different S. cerevisiae strains [56, 57]. In the present paper, we successfully exploited a combinatorial approach using all three random strain improvement strategies described above, in order to improve D-xylose fermentation efficiency of the recombinant industrial strain HDY.GUF5.
We first started with random mutagenesis of the recombinant strain to generate very diverse genetic variation that might establish initial D-xylose fermentation capacity. Selection of mutants with a significant D-xylose anaerobic fermentation rate is a challenging task, because likely multiple mutations are required . In addition, a previous study reported that direct selection of a mutant S. cerevisiae population capable of anaerobic D-xylose utilization, was unsuccessful . Therefore, we first selected clones from a heavily-mutagenized population that were able to grow at least to some extent on D-xylose medium as a sole carbon source. Since strong random mutagenesis likely results in both beneficial and deleterious mutations, we presumed that genetic recombination of the mutants obtained, with the original industrial strain by genome shuffling, and selection for D-xylose utilization capacity, would result in enrichment of beneficial and loss of unfavorable mutations . After only one step of genome shuffling, the whole shuffled culture already demonstrated a significantly improved rate of D-xylose fermentation. However, attempts to isolate single cell clones from this shuffled culture with better D-xylose utilization rate, compared to that of the best mutant strain M315, failed. Thus, we decided to enrich the clones with most rapid D-xylose utilization and at the same time further improve their rate of D-xylose utilization, through adaptive evolution in D-xylose medium. The selection of clones with a shorter lag phase on D-xylose and a higher D-xylose utilization rate is most obvious. However, clones that utilize a larger part of the D-xylose will be able to undergo more proliferation cycles and therefore will tend to be present in higher amounts and thus also preferentially transferred to the next culture. Since the cultures were semi-anaerobic, the D-xylose is largely converted to ethanol and therefore these clones will likely also have a higher ethanol yield.
After only two transfers in D-xylose medium under semi-anaerobic conditions, the D-xylose fermentation rate already increased dramatically. Subsequent serial transfers resulted in further gradual improvement of D-xylose utilization. In previous studies, evolutionary adaptation under aerobic conditions followed by gradual transition to anaerobic conditions, was necessary to obtain strains with anaerobic D-xylose utilization capacity. In addition, several generations were required to obtain strains with efficient D-xylose fermentation capacity [28, 55, 59]. In our study, even though the best isolate GS1.11-26 was isolated after 11 serial transfers, clones with high D-xylose utilization capacity could already be isolated after only 2 transfers. The rapid improvement in the rate of D-xylose fermentation might be explained by the presence of a suitable combination of important genetic changes introduced by the mutagenesis and genome shuffling, and sustaining rapid improvement of D-xylose utilization by a repetitive subsequent genetic modification, such as amplification of the XylA gene or another crucial genetic element, and/or rapid enrichment of clones with a superior combination of mutant alleles. An important genetic change might have been generated also in the second culture of the evolutionary adaptation, which was characterized by a sharp rise in CO2 evolution at the end, and a dramatic increase in the rate of fermentation when this culture was transferred to the next batch. During evolutionary engineering, expansions and contractions of different subpopulations can occur [60, 61] and an individual cell with a beneficial mutation, providing a relative fitness advantage, can develop into a dominant subpopulation after several generations in serial batch transfer experiments . In our work, high variability in the rate of D-xylose fermentation was observed among individual clones isolated from intermediate cultures in the evolutionary adaptation process. However, isolates from the last culture showed a very similar fermentation performance, although not precisely the same, suggesting that the fitter clones finally conquered and dominated the culture.
The best strain, GS1.11-26, showed a reproducible and stable D-xylose fermentation rate and was further characterized both in laboratory medium and in three industrially relevant lignocellulosic feedstocks. In synthetic medium with D-xylose as a sole carbon source, the GS1.11-26 strain showed a maximum specific D-xylose consumption rate at least 15 times higher than the previous industrial strain BWY10Xyl expressing the same codon-optimized C. phytofermentans XI . The GS1.11-26 strain also accomplished complete attenuation of D-xylose with an ethanol yield of 0.46 g/g D-xylose, whereas the previous strain BWY10Xyl left a substantial amount of D-xylose unfermented. Moreover, the yield of ethanol obtained with GS1.11-26 was higher than the yield obtained with the best strain reported recently . As a consequence, GS1.11-26 exhibited the highest D-xylose to ethanol conversion yield than any other recombinant strain of S. cerevisiae reported so far. The high ethanol yield can also be explained by the very low xylitol yield, which is remarkable since the GRE3 gene had not been deleted nor was it inactivated in the strain development programme. The low xylitol yield, in the absence of GRE3 inactivation, might be due to the inherently higher metabolic flux in the industrial bioethanol production strain Ethanol Red, compared to the previously used strain backgrounds.
The GS1.11-26 strain also performed very well in lignocellulose hydrolysates both in SHF and SSF. The yield of ethanol per g consumed sugars, was slightly higher in all the lignocellulose hydrolysates compared to that in synthetic and YP medium. This is probably due to the lower amount of xylitol and glycerol formed, and is consistent with previous results [46, 63]. In SHF, it reached high maximum D-xylose consumption rates of 1.1 g/g inoculum DW/h and it showed partial co-fermentation of glucose and D-xylose during separate hydrolysis and fermentation. We have used a parameter for calculation of the specific sugar consumption rate based on the initial inoculum density, since the whole slurry was used for the fermentation experiment and since it is difficult to estimate the biomass during the fermentation process.
The ethanol yield from glucose and D-xylose in lignocellulose hydrolysates was also close to maximum and final ethanol titers between 3.9 and 5.8% (v/v) were reached, depending on the type of hydrolysate. The GS1.11-26 strain maintained a high level of tolerance like its parent Ethanol Red in inhibitor rich spruce hydrolysate and to individual inhibitors HMF and furfural. However, the strain did not retain the same high ethanol tolerance as the original Ethanol Red parent strain, though it was still able to accumulate more than 15% ethanol in very high-gravity fermentation (YP + 330 g/L glucose). The relatively high tolerance of GS1.11-26 to inhibitors, like HMF and furfural, found in spruce hydrolysate, but its lower tolerance to other stresses, like ethanol and acetic acid, can be explained by the fact that, after the genome shuffling step spruce hydrolysate was used as selective medium. The cells that were able to grow in spruce hydrolysate were further used for the evolutionary adaptation. This result demonstrates the importance of the selection conditions during evolutionary engineering, which is in agreement with the principle, “you get what you screened for” . GS1.11-26 showed reduced tolerance to acetic acid compared to the parent HDY.GUF5. This can be explained by different mechanisms underlying tolerance to various inhibitors . In S. cerevisiae, the tolerance mechanism to HMF and furfural, is similar, but distinct from that of acetic acid .
SSF is an interesting process for production of ethanol from lignocellulosic feedstocks, e.g. because it strongly reduces feedback-inhibition on enzymatic hydrolysis by the liberated monosaccharides and also reduces the danger of contamination. SSF performed at higher temperature (39°C) was also shown to increase the final yield of ethanol, because of a better compromise between the temperature optima of the enzymes and the yeast . In this respect, GS1.11-26 performed very well with almost complete attenuation of both glucose and D-xylose in about 96 h at 39°C. In a previously reported SSF of Arundo hydrolysate using Ethanol Red , there was also some D-xylose consumption, but only as a result of D-xylose reduction to xylitol. In our study, the final ethanol concentration for GS1.11-26 was 20.3 g/L, corresponding to an ethanol yield of 0.29, to be compared to the previously reported values for Ethanol Red of 15.3 g/L and 0.22 g ethanol/g total sugar. The ethanol yield thus increased by about 32% due to the efficient D-xylose conversion. The increase in the ethanol yield was in fact slightly higher than the increase expected from the D-xylose conversion alone, possibly due to removal of D-xylose inhibition on enzymatic hydrolysis.
Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to cell extracts of the parent strain. However, there were no mutations in the XylA gene. Increased XI activity without any mutations in the XylA gene has also been reported recently [50, 51]. The high XI activity was explained by integration into the genome in multiple copies of the plasmid carrying the XylA gene . Although the recombinant strain in our work has been constructed through chromosomal integration of the XylA gene, it is possible that multiple chromosomal amplifications of the gene have occurred during the evolutionary adaptation process. The precise mechanism behind the establishment of the high XI activity in GS1.11-26 is currently being investigated and will be reported elsewhere.
Overexpression of XI in the parent strain did not increase the D-xylose consumption rate, as opposed to overexpression in the mutant strain M315 obtained after the mutagenesis step. This indicates that rapid D-xylose consumption requires a synergistic interaction between high XI activity and one or more mutations in the genome, which is in agreement with another report, in which high D-xylose assimilation capacity could only be attributed partially to the high activity of XI .
This clearly shows that the generation of other genetic changes, e.g. as obtained in our work by chemical mutagenesis, is essential for development of a pentose-utilizing strain with high performance. On the other hand, the random mutagenesis steps also resulted in unfavorable effects on other properties, such as reduced aerobic growth rate in glucose and a reduced glucose fermentation rate. This has also been reported previously during selection of a recombinant S. cerevisiae strain for anaerobic growth in D-xylose. In that report, strains exhibiting significant improvement in anaerobic D-xylose utilization also showed a reduced aerobic growth rate in glucose . We do not know whether the reduced glucose consumption rate or reduced aerobic growth rate in glucose, are trade-offs for the high D-xylose utilization capacity. Future research will have to show whether these negative side-effects are due to background mutations in the strain, which can be lost without affecting its high performance for D-xylose utilization, or whether they are causally linked to the high D-xylose fermentation rate. This will have important implications for further improvement of the strain for efficient co-fermentation of glucose, D-xylose and L-arabinose. In spite of this, the GS1.11-26 shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates. Moreover, it already contains the genes for additional utilization of L-arabinose and should be easily evolved also for efficient fermentation of this pentose sugar.
We have developed a robust industrial S. cerevisiae strain exhibiting the highest yield of ethanol from D-xylose. The high D-xylose fermentation capacity was completely stable after many generations of growth in the absence of D-xylose. High activity of XI was found to be the main but not the only reason for fast D-xylose assimilation capacity. The final evolved strain also demonstrated an efficient fermentation rate of glucose and D-xylose in inhibitor-rich lignocellulose hydrolysates. However, the evolved strain GS1.11-26 showed a partial respiratory defect causing a reduced aerobic growth rate and it also had a slightly reduced glucose fermentation rate. GS1.11-26 has a significant potential for further development of a robust industrial yeast strain for bioethanol production with various lignocellulose hydrolysates.
Strains and growth conditions
S. cerevisiae strains used in the study
Industrial bioethanol production strain, MAT a /α
Fermentis, a division of S. I. Lesaffre, Lille, France
Ethanol Red; pyk2::XylA; XKS1; TAL1; TKL1; RPE1; RKI1; HXT7;AraT; AraA; AraB;AraD; TAL2; TKL2
HDY.GUF5 + 3 h mutagenesis in 3% EMS, MATα/α
HDY.GUF5 + 4 h mutagenesis in 3% EMS, MAT a /α
HDY.GUF5, M315 and M492 + genome shuffling and evolutionary adaptation, MATα/α
USM21 HIS3::YIpXR/XDH/XK + mutagenesis and selection
Mutagenesis and genome shuffling
Overnight-grown yeast cells were harvested, washed twice with phosphate buffer (pH 7), and re-suspended in 1 ml sodium phosphate buffer pH 7 at a cell concentration of 2 × 108 cells/ml. Five different samples were treated with a final concentration of 3% Ethyl Methanesulfonate (EMS) or only phosphate buffer (as control) for different time intervals at 30°C. The EMS was subsequently neutralized by washing twice with freshly prepared 5% sodium thiosulphate. The cell pellets were then re-suspended in sterile 500 μl milliQ water and plated in aliquots of 100 μl onto both YPX and YPD plates. To estimate the percentage survival after mutagenesis, colonies of EMS treated cells from the YPD plates were counted and the ratio relative to that of untreated cells was calculated.
For genome shuffling, cells selected based on growth on D-xylose and sporulation efficiency were sporulated in 1% potassium acetate medium. After 7 days at 23°C, asci were harvested and spores were purified . The purified spores from each strain were mixed together and allowed to germinate for 2 h in YPD medium. Exponentially growing cells from a MAT α/α diploid strain (M315) were mixed with the germinated spores. The cells were allowed to mate in 40 ml YPD in a shaking incubator at 70 rpm for 48 h. To select D-xylose growing strains, the zygotes were subsequently transferred to YP medium containing D-xylose as a sole carbon source. The D-xylose growing cells were inoculated into the liquid fraction of acid pretreated spruce hydrolysate at three different concentrations (40%, 50% and 60%). To maintain the D-xylose growth phenotype, 40 g/L D-xylose was added to the spruce hydrolysate medium. Cells growing in the highest concentration of hydrolysate were grown again in YP medium containing D-xylose and subsequently used to start the evolutionary adaptation by sequential batch cultivation.
Determination of mating type
Determination of the mating type was done by PCR and pheromone assay. PCR was performed with a primer for the MAT locus and a MAT a or MATα specific primer . To validate mating type by a pheromone assay, two tester strains of S. cerevisiae, MATa bar1-∆ and MATα sst2-∆, were used. A small amount of tester strain was mixed with 1% agar at 50°C and immediately poured on top of a YPD plate. After the top agar solidified, about 10 μl of cell suspension from strains to be tested was spotted onto each tester plate. After 24 h incubation at 30°C, MATα cells showed a zone of growth inhibition on plates of the bar1-∆ strain while MATa cells showed a zone of growth inhibition on plates of the sst2-∆ strain. Diploid cells did not produce a zone of inhibition.
Molecular Biology methods
Yeast cells were transformed with the LiAc/SS-DNA/PEG method [68, 69]. Genomic DNA from yeast was extracted with PCI [phenol/chloroform/isoamyl-alcohol (25:24:1)] . Polymerase chain reaction (PCR) was performed with Phusion DNA polymerase (New England Biolabs) for construction of the vectors and sequencing purposes and ExTaq (Takara) or Taq (NEB) for diagnostic purposes. Sanger sequencing was performed by the Genetic Service Facility of the VIB.
Plasmids were propagated in E. coli strain TOP10 (Invitrogen) or DH5α (NEB), grown in LB medium, containing 100 μg/ml ampicillin at 30°C or 37°C. E. coli cells were transformed using the CaCl2  or electroporation method . The plasmids pHD8 and pHD22 were constructed by homologous recombination in yeast from up to 17 single overlapping PCR fragments. The templates used were genomic DNA from S. cerevisiae, the plasmids pUG6 , pZC1 , p426H-i-opt.XI , YEparaAsynth and YEparaDsynth  as well as the codon-optimized genes of XKS1 and E.coli araB (method described in  - Sloning BioTechnology) and NQM1 and TKL2 (DNA2.0). The assembly of the multi-copy plasmid carrying the XylA gene, was similar to the plasmid pHD8, but the genes flanked by the i1 and i3 regions (see Figure 1a) were substituted by restriction digestion and ligation with one copy of the XylA gene.
Determination of ploidy by flow cytometry
Flow cytometry analysis of DNA content was performed according to Popolo et al. . Briefly, exponentially growing cells were washed with ice-cold sterile water and fixed with 70% ethanol. Cells were treated with RNase (1 mg/ml) and the DNA was stained with propidium iodide (0.046 M) in 50 mM Tris, pH 7.7 and 15 mM MgCl2, at 4°C for about 48 h. The fluorescence intensity was measured using a FACScan instrument (Becton Dickinson).
Determination of specific D-xylose isomerase activity
The specific activity of D-xylose isomerase was measured based on the isomerization of D-xylose to xylulose, followed by reduction of xylulose to xylitol by sorbitol dehydrogenase . Cell extraction was performed by disruption with glass beads using a Fast Prep homogenizer. Protein concentration was determined using the Pierce 660 nm Protein Assay kit (Thermo Scientific) according to the manufacturer’s manual. XI activity in the fresh cell extract was determined at 30°C. The assay mixture contained 100 mM Tris–HCl buffer (pH 7.5), 10 mM MgCl2, 0.15 mM NADH and 2U sorbitol dehydrogenase. The reaction was started by addition of D-xylose to a final concentration of 500 mM. A molar extinction coefficient of 6.25 (mM cm)-1 at 340 nm for NADH was used to calculate specific activity. Specific activity was expressed as Units per mg protein. One unit corresponds to the conversion of 1 μM of substrate into product in one min under the specified reaction conditions.
Semi-anaerobic sequential batch fermentations were performed in 100 ml YP medium containing 40 to 100 g/L D-xylose as sole carbon source, in cylindrical tubes with cotton plugged rubber stopper and glass tubing. Cultures were continuously stirred magnetically at 120 rpm and incubated at 35°C. Semi-anaerobic batch fermentations in synthetic or complex medium were performed in 300 ml shake flasks with a working volume of 200 ml at 35°C. Flasks were closed with fermentation locks containing glycerol. Nitrogen gas was sparged after cell inoculation until the oxygen concentration reached about 2 ppm. Cultures were continuously stirred at 120 rpm using a magnetic stirrer. Samples were taken every few hours with needles.
Inhibitor tolerance assay
Tolerance to osmotic and ethanol stress was performed with solid medium [77, 78]. Strains were inoculated in YPD medium and grown at 30°C for 2 days until stationary phase. Cultures were diluted to an OD600 of 0.5, and 5 μl of a twofold dilution was spotted on YPD plates containing different concentrations of sorbitol or ethanol. Sorbitol was used to generate high osmotic stress. The growth was examined after 2 days for YPD control medium, or 6 to 10 days for plates containing sorbitol or ethanol.
Tolerance to HMF, furfural and acetate was performed in 1 ml liquid synthetic medium containing the individual inhibitors in a 24-well plate. The same pre-culture used for the spot assay was inoculated into medium containing a range of concentrations of each inhibitor at an initial OD630 of 0.2. The OD was measured after 48 to 72 h using Synergy H1 Hybrid Reader (BioTek, Winooski, VT, USA). Each experiment was performed in duplicate with independent cultures.
Origin and preparation of lignocellulose hydrolysates
Three different pretreated lignocellulosic biomass materials (Arundo donax, spruce tree and a 50/50 mixture of wheat straw and hay) were used to evaluate the fermentation performance of the final strain. They were obtained from Chemtex (Tortona AL, Italy), SEKAB E-Technology AB (Örnsköldsvik, Sweden), and KaHo Sint-Lieven (Ghent, Belgium), respectively. Pretreatment of Arundo donax and spruce were performed by pure steam explosion and SO2 impregnated steam explosion, respectively. The wheat straw/hay mixture was pretreated using 0.4 M NaOH at 25°C for 24 h. The residue was washed 3 times with RO water. The Arundo donax and spruce pretreated materials were hydrolyzed at an initial pH of 4.8, using enzyme complex ACCELLERASE® 1500 for 48 h at 53°C according to the protocol from the manufacturer. Enzyme hydrolysis of pretreated wheat straw/hay mixture was done using Novozymes cellulase complex (NS50013) and beta-glucosidase (NS50010) at 50°C, pH 4.5 for 24 h. Fermentation was done at a solid loading of 12% (w/v) for spruce and Arundo donax hydrolysate and 19% (w/v) for wheat straw/hay hydrolysate. For selection of D-xylose growing and inhibitor tolerant strains after the genome shuffling step, pretreated spruce material was used before enzymatic hydrolysis.
Simultaneous Saccharification and Fermentation (SSF)
All SSF experiments were carried out in 2.5 L bioreactors (Biostat A, B. Braun Biotech International, Melsungen, Germany and Biostat A plus, Sartorius, Melsungen, Germany) with a final working weight of 1.2 kg. The experiments were carried out with an initial water insoluble solids (WIS) content of 10% according to . The same batches of pretreated spruce and arundo were used as in . The full composition of the pretreated material is given in that reference. To obtain the desired WIS content, the pretreatment slurry was diluted with sterile deionized water. The pH was maintained at 5.0 throughout the fermentation by automatic addition of 3 M NaOH and the stirring speed was kept at 500 rpm. Celluclast 1.5 L, and Novozym 188, a β-glucosidase provided by Novozymes A/S (Bagsvaerd, Denmark) were used and the enzyme dosage for SSF experiments was 10 mg/g WIS for Celluclast 1.5 L and 500 nkat/g DW for Novozym 188. The SSF medium was supplemented with 0.5 g/L (NH4)2HPO4, 0.025 g/L MgSO4 · 7H2O and 1.0 g/L yeast extract. An initial yeast concentration of 4 g DW/L was used. All SSF experiments were performed in duplicate. The initial D-xylose content in GS1.11-26 experiments on Arundo was higher than in the corresponding previous experiments with Ethanol Red . The reason was that the time for autoclaving the slurry was increased from 20 min to 1 h prior to SSF to prevent contamination, which caused hydrolysis of xylo-oligomers.
The yeast to be used in SSF was obtained by propagation from solid YPD medium into aerobic batch cultivation on glucose, followed by aerobic fed-batch cultivation on arundo or spruce liquid fractions. A defined medium with glucose 20 g/L as the carbon source  was used for the batch phase. However, no uracil was added in the present case. The volume in the bioreactor was 0.7 L and pH was maintained at 5.0 throughout the cultivation by automatic addition of 3 M NaOH. The cultivation was initiated by adding 20.0 mL of inoculum (prepared according to ) to the bioreactor. Aeration was maintained at 1.2 L/min and the stirrer speed was kept at 800 rpm. The oxygen and CO2 content in the exhaust gas were measured with a gas analyzer (1313 Fast Response Triple-gas Monitor, INNOVA, Denmark). Upon depletion of the ethanol produced in the batch phase, the feeding of liquid fraction from spruce or Arundo was initiated. A total of 1.0 L of autoclaved liquid fraction was used for feeding. In case of arundo, 40 g of glucose was added to 1.0 L of liquid fraction prior to autoclaving. The feeding followed a linear profile with an initial feed rate of 0.04 L/h which was increased linearly to 0.10 L/h during 16 h of cultivation according to . The aeration during the fed-batch phase was maintained at 1.4 L/min and the stirrer speed was kept at 800 rpm. After cultivation, the cells were harvested by centrifugation in 700 mL flasks for 8 min at 3000 rpm using a HERMLE Z 513 K centrifuge (HERMLE Labortechnik, Wehingen, Germany). The pellets were resuspended in 0.9% NaCl solution in order to obtain a cell suspension with a cell mass concentration of 75 g DW/L.
Analysis of substrates and metabolites
The metabolites and substrate content were analysed using high performance liquid chromatography (HPLC). In the case of hydrolysates, samples were centrifuged in 2 mL microcentrifuge tubes at 14,000 rpm for 5 min (Z 160 M, HERMLE Labortechnik, Wehingen, Germany). The supernatant was filtered using 0.2 μm filters, and the filtered samples were stored at −20°C. The sugar concentrations were determined using a polymer column (Aminex HPX87P, BioRad Laboratories, München, Germany) at 85°C. MilliQ water was used as eluent, with a flow rate of 0.6 ml/min. Ethanol, glycerol, acetate, HMF and furfural were analyzed using an Aminex HPX87H column (BioRad Laboratories, München, Germany) at 60°C. The eluent was 5 mM H2SO4 with a flow rate of 0.6 ml/min. The compounds of interest were detected with a refractive index detector (Waters 2410, Waters, Milford, MA, USA) or with a UV detector at a wavelength of 210 nm (Waters 2487, Waters, Milford, MA, USA). Metabolites and substrates in fermentation experiments with synthetic or complex medium were analyzed by Waters Isocratic Breeze HPLC system using ion-exchange column WAT010290 and a refractive index detection system (Waters 2414 RI detector). Column temperature was maintained at 75°C and 5 mM H2SO4 was used as eluent at a flow rate of 1 ml/min.
Cell mass concentration
Optical Density (OD600nm) was used to estimate cell dry weight (DW). The DW for inocula was measured by filtering a 10 ml culture aliquot in pre-weighed 0.2 mm Supor Membrane disc filters (PALL Corporation, USA), washing the filter with MilliQ water, and drying it in a microwave oven at about 150 watt for 15–20 min to constant weight. The correlation between dry weight (DW) and OD600 was measured for each strain tested.
Ethanol yield in SSF was calculated based on the total amount of fermentable sugars, which includes glucose, mannose, and galactose, present in the pretreatment slurry, including monomers, oligomers, and polymers (glucan fibers). In SHF, the total amount of fermentable sugar monomers was taken into account. The specific D-xylose consumption rate was calculated according to the standard protocol described previously . The biomass of the initial inoculum was used for calculation of sugar consumption in the fermentation experiments with lignocellulose hydrolysates, since the biomass cannot be accurately measured during the actual fermentation process.
Yeast extract peptone dextrose
Yeast extract peptone D-xylose
synthetic complete medium
high performance liquid chromatography
very high gravity
polymerase chain reaction
Simultaneous saccharification and fermentation
Separate hydrolysis and fermentation.
We wish to thank Stijn De Graeve, Jean-Paul Meijnen, Georg Hubmann, Yudi Yang, Ben Souffriau and all other members of the Genetic Analysis Group at VIB/KU Leuven for stimulating discussions, Paul Vandecruys for technical support and Nico Vangoethem for informatics support. We are also grateful to Carl-Axel Lalander, Torbjörn van der Meulen and Sune Wännström (Sekab E-Technology, Örnsköldsvik, Sweden) and Tommaso di Felice (Chemtex Italia srl, Tortona AL, Italy) for kind provision of lignocellulose hydrolysates, and Marie-Françoise Gorwa-Grauslund for the strain TMB3400. This work has been supported by a predoctoral fellowship from the KU Leuven Interfaculty Council for Development Cooperation (IRO) to MD and from the China Scholarship Council to YL, SBO grant (IWT 90043) from IWT-Flanders, the EC 7th Framework program (NEMO project) and IOF-Knowledge platform (IKP/10/002 ZKC 1836) to JMT. Work in the laboratory of EB has been additionally supported financially by Butalco GmbH (Switzerland).
- Zaldivar J, Nielsen J, Olsson L: Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration. Appl Microbiol Biotechnol 2001, 56: 17-34. 10.1007/s002530100624View ArticleGoogle Scholar
- Lau MW, Gunawan C, Balan V, Dale BE: Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production. Biotechnol Biofuels 2010, 3: 11. 10.1186/1754-6834-3-11View ArticleGoogle Scholar
- Ebringerová A, Hromádková Z, Heinze T: Hemicellulose. In Polysaccharides I. Volume 186. Edited by: Heinze T. Berlin. Heidelberg: Springer-Verlag; 2013:1-67.Google Scholar
- Hahn-Hagerdal B, Karhumaa K, Fonseca C, Spencer-Martins I, Gorwa-Grauslund MF: Towards industrial pentose-fermenting yeast strains. Appl Microbiol Biotechnol 2007, 74: 937-953. 10.1007/s00253-006-0827-2View ArticleGoogle Scholar
- Weber C, Farwick A, Benisch F, Brat D, Dietz H, Subtil T, Boles E: Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels. Appl Microbiol Biotechnol 2010, 87: 1303-1315. 10.1007/s00253-010-2707-zView ArticleGoogle Scholar
- Almeida JR, Modig T, Petersson A, Hahn-Hagerdal B, Liden G, Gorwa-Grauslund MF: Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae . J Chem Technol Biotechnol 2007, 82: 340-349. 10.1002/jctb.1676View ArticleGoogle Scholar
- Miller EN, Jarboe LR, Turner PC, Pharkya P, Yomano LP, York SW, Nunn D, Shanmugam KT, Ingram LO: Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 2009, 75: 6132-6141. 10.1128/AEM.01187-09View ArticleGoogle Scholar
- Huang CF, Lin TH, Guo GL, Hwang WS: Enhanced ethanol production by fermentation of rice straw hydrolysate without detoxification using a newly adapted strain of Pichia stipitis . Bioresour Technol 2009, 100: 3914-3920. 10.1016/j.biortech.2009.02.064View ArticleGoogle Scholar
- Hahn-Hagerdal B, Karhumaa K, Jeppsson M, Gorwa-Grauslund MF: Metabolic engineering for pentose utilization in Saccharomyces cerevisiae . Adv Biochem Eng Biotechnol 2007, 108: 147-177.Google Scholar
- Nevoigt E: Progress in metabolic engineering of Saccharomyces cerevisiae . Microbiol Mol Biol Rev 2008, 72: 379-412. 10.1128/MMBR.00025-07View ArticleGoogle Scholar
- Jeppsson M, Bengtsson O, Franke K, Lee H, Hahn-Hagerdal B, Gorwa-Grauslund MF: The expression of a Pichia stipitis xylose reductase mutant with higher K(M) for NADPH increases ethanol production from xylose in recombinant Saccharomyces cerevisiae . Biotechnol Bioeng 2006, 93: 665-673. 10.1002/bit.20737View ArticleGoogle Scholar
- Johansson B, Christensson C, Hobley T, Hahn-Hagerdal B: Xylulokinase overexpression in two strains of Saccharomyces cerevisiae also expressing xylose reductase and xylitol dehydrogenase and its effect on fermentation of xylose and lignocellulosic hydrolysate. Appl Environ Microbiol 2001, 67: 4249-4255. 10.1128/AEM.67.9.4249-4255.2001View ArticleGoogle Scholar
- Johansson B, Hahn-Hagerdal B: The non-oxidative pentose phosphate pathway controls the fermentation rate of xylulose but not of xylose in Saccharomyces cerevisiae TMB3001. FEMS Yeast Res 2002, 2: 277-282.Google Scholar
- Bengtsson O, Hahn-Hagerdal B, Gorwa-Grauslund MF: Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae . Biotechnol Biofuels 2009, 2: 9. 10.1186/1754-6834-2-9View ArticleGoogle Scholar
- Runquist D, Hahn-Hagerdal B, Bettiga M: Increased ethanol productivity in xylose-utilizing Saccharomyces cerevisiae via a randomly mutagenized xylose reductase. Appl Environ Microbiol 2010, 76: 7796-7802. 10.1128/AEM.01505-10View ArticleGoogle Scholar
- Olofsson K, Runquist D, Hahn-Hagerdal B, Liden G: A mutated xylose reductase increases bioethanol production more than a glucose/xylose facilitator in simultaneous fermentation and co-fermentation of wheat straw. AMB Express 2011, 1: 4. 10.1186/2191-0855-1-4View ArticleGoogle Scholar
- Peng B, Shen Y, Li X, Chen X, Hou J, Bao X: Improvement of xylose fermentation in respiratory-deficient xylose-fermenting Saccharomyces cerevisiae . Metab Eng 2012, 14: 9-18. 10.1016/j.ymben.2011.12.001View ArticleGoogle Scholar
- Walfridsson M, Bao X, Anderlund M, Lilius G, Bulow L, Hahn-Hagerdal B: Ethanolic fermentation of xylose with Saccharomyces cerevisiae harboring the Thermus thermophilus xylA gene, which expresses an active xylose (glucose) isomerase. Appl Environ Microbiol 1996, 62: 4648-4651.Google Scholar
- Kuyper M, Harhangi HR, Stave AK, Winkler AA, Jetten MS, De Laat WT, Den Ridder JJ, Op Den Camp HJ, Van Dijken JP, Pronk JT: High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae . FEMS Yeast Res 2003, 4: 69-78. 10.1016/S1567-1356(03)00141-7View ArticleGoogle Scholar
- Kuyper M, Hartog MM, Toirkens MJ, Almering MJ, Winkler AA, Van Dijken JP, Pronk JT: Metabolic engineering of a xylose-isomerase-expressing Saccharomyces cerevisiae strain for rapid anaerobic xylose fermentation. FEMS Yeast Res 2005, 5: 399-409. 10.1016/j.femsyr.2004.09.010View ArticleGoogle Scholar
- Bettiga M, Hahn-Hagerdal B, Gorwa-Grauslund MF: Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains. Biotechnol Biofuels 2008, 1: 16. 10.1186/1754-6834-1-16View ArticleGoogle Scholar
- Chang Q, Griest TA, Harter TM, Petrash JM: Functional studies of aldo-keto reductases in Saccharomyces cerevisiae . Biochim Biophys Acta 2007, 1773: 321-329. 10.1016/j.bbamcr.2006.10.009View ArticleGoogle Scholar
- Traff KL, Jonsson LJ, Hahn-Hagerdal B: Putative xylose and arabinose reductases in Saccharomyces cerevisiae . Yeast 2002, 19: 1233-1241. 10.1002/yea.913View ArticleGoogle Scholar
- Toivari MH, Salusjarvi L, Ruohonen L, Penttila M: Endogenous xylose pathway in Saccharomyces cerevisiae . Appl Environ Microbiol 2004, 70: 3681-3686. 10.1128/AEM.70.6.3681-3686.2004View ArticleGoogle Scholar
- Traff KL, Otero Cordero RR, Van Zyl WH, Hahn-Hagerdal B: Deletion of the GRE3 aldose reductase gene and its influence on xylose metabolism in recombinant strains of Saccharomyces cerevisiae expressing the xylA and XKS1 genes. Appl Environ Microbiol 2001, 67: 5668-5674. 10.1128/AEM.67.12.5668-5674.2001View ArticleGoogle Scholar
- Aguilera J, Prieto JA: The Saccharomyces cerevisiae aldose reductase is implied in the metabolism of methylglyoxal in response to stress conditions. Curr Genet 2001, 39: 273-283. 10.1007/s002940100213View ArticleGoogle Scholar
- Brat D, Boles E, Wiedemann B: Functional expression of a bacterial xylose isomerase in Saccharomyces cerevisiae . Appl Environ Microbiol 2009, 75: 2304-2311. 10.1128/AEM.02522-08View ArticleGoogle Scholar
- Kuyper M, Toirkens MJ, Diderich JA, Winkler AA, Van Dijken JP, Pronk JT: Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Res 2005, 5: 925-934. 10.1016/j.femsyr.2005.04.004View ArticleGoogle Scholar
- Wisselink HW, Toirkens MJ, Wu Q, Pronk JT, Van Maris AJ: Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Appl Environ Microbiol 2009, 75: 907-914. 10.1128/AEM.02268-08View ArticleGoogle Scholar
- Karhumaa K, Wiedemann B, Hahn-Hagerdal B, Boles E, Gorwa-Grauslund MF: Co-utilization of L-arabinose and D-xylose by laboratory and industrial Saccharomyces cerevisiae strains. Microb Cell Fact 2006, 5: 18. 10.1186/1475-2859-5-18View ArticleGoogle Scholar
- Van Maris AJ, Winkler AA, Kuyper M, De Laat WT, Van Dijken JP, Pronk JT: Development of efficient xylose fermentation in Saccharomyces cerevisiae : xylose isomerase as a key component. Adv Biochem Eng Biotechnol 2007, 108: 179-204.Google Scholar
- Boles E, Schulte F, Miosga T, Freidel K, Schluter E, Zimmermann FK, Hollenberg CP, Heinisch JJ: Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate. J Bacteriol 1997, 179: 2987-2993.Google Scholar
- Wiedemann B, Boles E: Codon-optimized bacterial genes improve L-arabinose fermentation in recombinant Saccharomyces cerevisiae . Appl Environ Microbiol 2008, 74: 2043-2050. 10.1128/AEM.02395-07View ArticleGoogle Scholar
- Hamacher T, Becker J, Gardonyi M, Hahn-Hagerdal B, Boles E: Characterization of the xylose-transporting properties of yeast hexose transporters and their influence on xylose utilization. Microbiology 2002, 148: 2783-2788.View ArticleGoogle Scholar
- Subtil T, Boles E: Competition between pentoses and glucose during uptake and catabolism in recombinant Saccharomyces cerevisiae . Biotechnol Biofuels 2012, 5: 14. 10.1186/1754-6834-5-14View ArticleGoogle Scholar
- Wisselink HW, Toirkens MJ, Del Rosario Franco Berriel M, Winkler AA, Van Dijken JP, Pronk JT, Van Maris AJ: Engineering of Saccharomyces cerevisiae for efficient anaerobic alcoholic fermentation of L-arabinose. Appl Environ Microbiol 2007, 73: 4881-4891. 10.1128/AEM.00177-07View ArticleGoogle Scholar
- Wahlbom CF, Van Zyl WH, Jonsson LJ, Hahn-Hagerdal B, Otero RR: Generation of the improved recombinant xylose-utilizing Saccharomyces cerevisiae TMB 3400 by random mutagenesis and physiological comparison with Pichia stipitis CBS 6054. FEMS Yeast Res 2003, 3: 319-326. 10.1016/S1567-1356(02)00206-4View ArticleGoogle Scholar
- Kuhn A, Van Zyl C, Van Tonder A, Prior BA: Purification and partial characterization of an aldo-keto reductase from Saccharomyces cerevisiae . Appl Environ Microbiol 1995, 61: 1580-1585.Google Scholar
- Zhang JG, Liu XY, He XP, Guo XN, Lu Y, Zhang BR: Improvement of acetic acid tolerance and fermentation performance of Saccharomyces cerevisiae by disruption of the FPS1 aquaglyceroporin gene. Biotechnol Lett 2011, 33: 277-284. 10.1007/s10529-010-0433-3View ArticleGoogle Scholar
- Bellido C, Bolado S, Coca M, Lucas S, Gonzalez-Benito G, Garcia-Cubero MT: Effect of inhibitors formed during wheat straw pretreatment on ethanol fermentation by Pichia stipitis . Bioresour Technol 2011, 102: 10868-10874. 10.1016/j.biortech.2011.08.128View ArticleGoogle Scholar
- Bellissimi E, Van Dijken JP, Pronk JT, Van Maris AJ: Effects of acetic acid on the kinetics of xylose fermentation by an engineered, xylose-isomerase-based Saccharomyces cerevisiae strain. FEMS Yeast Res 2009, 9: 358-364. 10.1111/j.1567-1364.2009.00487.xView ArticleGoogle Scholar
- Wright J, Bellissimi E, De Hulster E, Wagner A, Pronk JT, Van Maris AJ: Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae . FEMS Yeast Res 2011, 11: 299-306. 10.1111/j.1567-1364.2011.00719.xView ArticleGoogle Scholar
- Persson P, Larsson S, Jonsson LJ, Nilvebrant NO, Sivik B, Munteanu F, Thorneby L, Gorton L: Supercritical fluid extraction of a lignocellulosic hydrolysate of spruce for detoxification and to facilitate analysis of inhibitors. Biotechnol Bioeng 2002, 79: 694-700. 10.1002/bit.10324View ArticleGoogle Scholar
- Ask M, Olofsson K, Felice TD, Ruohonen L, Penttilä M, Lidén G, Olsson L: Challenges in enzymatic hydrolysis and fermentation of pretreated Arundo donax revealed by a comparison between SHF and SSF. Process Biochem 2012, 47: 1452-1459. 10.1016/j.procbio.2012.05.016View ArticleGoogle Scholar
- Mutturi S, Liden G: Effect of temperature on simultaneous saccharification and fermentation of pretreated spruce and arundo. Ind Eng Chem Res 2013, 52: 1244-1251. 10.1021/ie302851wView ArticleGoogle Scholar
- Olofsson K, Rudolf A, Liden G: Designing simultaneous saccharification and fermentation for improved xylose conversion by a recombinant strain of Saccharomyces cerevisiae . J Biotechnol 2008, 134: 112-120. 10.1016/j.jbiotec.2008.01.004View ArticleGoogle Scholar
- Liu JJ, Ding WT, Zhang GC, Wang JY: Improving ethanol fermentation performance of Saccharomyces cerevisiae in very high-gravity fermentation through chemical mutagenesis and meiotic recombination. Appl Microbiol Biotechnol 2011, 91: 1239-1246. 10.1007/s00253-011-3404-2View ArticleGoogle Scholar
- Pais TM, Foulquié-Moreno MR, Hubmann G, Duitama J, Swinnen S, Goovaerts A, Yang Y, Dumortier F, Thevelein JM: Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast. PLoS Genet 2013,9(6):e1003548. 10.1371/journal.pgen.1003548View ArticleGoogle Scholar
- Bellissimi E, Richards C: Yeast propagation. In The alcohol textbook, a reference for the beverage, fuel and industrial alcohol industries. 5th edition. Edited by: Ingledew WM, Kelsall DR, Austin GD, Kluhspies C. Nottingham: University Press; 2009:145-159.Google Scholar
- Shen Y, Chen X, Peng B, Chen L, Hou J, Bao X: An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile. Appl Microbiol Biotechnol 2012, 96: 1079-1091. 10.1007/s00253-012-4418-0View ArticleGoogle Scholar
- Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G: Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae . Metab Eng 2012, 14: 611-622. 10.1016/j.ymben.2012.07.011View ArticleGoogle Scholar
- Chu BC, Lee H: Genetic improvement of Saccharomyces cerevisiae for xylose fermentation. Biotechnol Adv 2007, 25: 425-441.View ArticleGoogle Scholar
- Hector RE, Dien BS, Cotta MA, Qureshi N: Engineering industrial Saccharomyces cerevisiae strains for xylose fermentation and comparison for switchgrass conversion. J Ind Microbiol Biotechnol 2011, 38: 1193-1202. 10.1007/s10295-010-0896-1View ArticleGoogle Scholar
- Liu E, Hu Y: Construction of a xylose-fermenting Saccharomyces cerevisiae strain by combined approaches of genetic engineering, chemical mutagenesis and evolutionary adaptation. Biochem Eng J 2010, 48: 204-210. 10.1016/j.bej.2009.10.011View ArticleGoogle Scholar
- Sonderegger M, Sauer U: Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol 2003, 69: 1990-1998. 10.1128/AEM.69.4.1990-1998.2003View ArticleGoogle Scholar
- Jingping G, Hongbing S, Gang S, Hongzhi L, Wenxiang P: A genome shuffling-generated Saccharomyces cerevisiae isolate that ferments xylose and glucose to produce high levels of ethanol. J Ind Microbiol Biotechnol 2012, 39: 777-787. 10.1007/s10295-011-1076-7View ArticleGoogle Scholar
- Zhang W, Geng A: Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method. Biotechnol Biofuels 2012, 5: 46. 10.1186/1754-6834-5-46View ArticleGoogle Scholar
- Gong J, Zheng H, Wu Z, Chen T, Zhao X: Genome shuffling: Progress and applications for phenotype improvement. Biotechnol Adv 2009, 27: 996-1005.View ArticleGoogle Scholar
- Kuyper M, Winkler AA, Van Dijken JP, Pronk JT: Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle. FEMS Yeast Res 2004, 4: 655-664. 10.1016/j.femsyr.2004.01.003View ArticleGoogle Scholar
- Reyes LH, Winkler J, Kao KC: Visualizing evolution in real-time method for strain engineering. Front Microbiol 2012, 3: 198.View ArticleGoogle Scholar
- Almario MP: Reyes LH. Kao KC: Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng; 2013.Google Scholar
- Elena SF, Lenski RE: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 2003, 4: 457-469.View ArticleGoogle Scholar
- Karhumaa K, Garcia Sanchez R, Hahn-Hagerdal B, Gorwa-Grauslund MF: Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant. Saccharomyces cerevisiae. Microb Cell Fact 2007., 6:Google Scholar
- Schmidt-Dannert C, Arnold FH: Directed evolution of industrial enzymes. Trends Biotechnol 1999, 17: 135-136. 10.1016/S0167-7799(98)01283-9View ArticleGoogle Scholar
- Palmqvist E, Hahn-Hägerdal B: Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition. Bioresour Technol 2000, 74: 25-33. 10.1016/S0960-8524(99)00161-3View ArticleGoogle Scholar
- Hou L: Novel methods of genome shuffling in Saccharomyces cerevisiae . Biotechnol Lett 2009, 31: 671-677. 10.1007/s10529-009-9916-5View ArticleGoogle Scholar
- Huxley C, Green ED, Dunham I: Rapid assessment of S. cerevisiae mating type by PCR. Trends Genet 1990, 6: 236.View ArticleGoogle Scholar
- Gietz RD, Schiestl RH, Willems AR, Woods RA: Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast 1995, 11: 355-360. 10.1002/yea.320110408View ArticleGoogle Scholar
- Gietz RD, Schiestl RH: High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc 2007, 2: 31-34. 10.1038/nprot.2007.13View ArticleGoogle Scholar
- Hoffman CS, Winston F: A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli . Gene 1987, 57: 267-272. 10.1016/0378-1119(87)90131-4View ArticleGoogle Scholar
- Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. 2nd edition. New York: Cold Spring Harbor; 1989.Google Scholar
- Dower WJ, Miller JF, Ragsdale CW: High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 1988, 16: 6127-6145. 10.1093/nar/16.13.6127View ArticleGoogle Scholar
- Guldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH: A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 1996, 24: 2519-2524. 10.1093/nar/24.13.2519View ArticleGoogle Scholar
- Carter Z, Delneri D: New generation of loxP-mutated deletion cassettes for the genetic manipulation of yeast natural isolates. Yeast 2010, 27: 765-775. 10.1002/yea.1774View ArticleGoogle Scholar
- Popolo L, Vanoni M, Alberghina L: Control of the yeast cell cycle by protein synthesis. Exp Cell Res 1982, 142: 69-78. 10.1016/0014-4827(82)90410-4View ArticleGoogle Scholar
- Kersters-Hilderson H, Callens M, Van Opstal O, Vangrysperre W, De Bruyne CK: Kinetic characterization of D-xylose isomerases by enzymatic assays ising D-sorbitol dehydrogenase. Enzyme Microb Technol 1987, 9: 145-148. 10.1016/0141-0229(87)90067-6View ArticleGoogle Scholar
- Leitão L, Prista C, Moura TF, Loureiro-Dias MC, Soveral G: Grapevine aquaporins: gating of a tonoplast intrinsic protein (TIP2;1) by cytosolic pH. PLoS One 2012, 7: e33219. 10.1371/journal.pone.0033219View ArticleGoogle Scholar
- Swinnen S, Schaerlaekens K, Pais T, Claesen J, Hubmann G, Yang Y, Demeke M, Foulquie-Moreno MR, Goovaerts A, Souvereyns K, et al.: Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res 2012, 22: 975-984. 10.1101/gr.131698.111View ArticleGoogle Scholar
- Bertilsson M, Olofsson K, Liden G: Prefermentation improves xylose utilization in simultaneous saccharification and co-fermentation of pretreated spruce. Biotechnol Biofuels 2009, 2: 8. 10.1186/1754-6834-2-8View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.