Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives

Sortase A-Mediated Ligation Facilitates Metabolic Channeling in Saccharomyces cerevisiae

Although the yeast Saccharomyces cerevisiae has been utilized for the bioproduction of various valuable substances, improving product concentration and production rate remains a challenge in its practical application. In this respect, metabolic channeling represents a potential strategy for addressing this issue. In the metabolic pathway for synthesizing a target product, closing enzymes induce substrate channeling, in which intermediates are transferred to the following enzyme to facilitate processing. To close enzymes in proximity, protein ligation is one of the solutions. However, genetic fusion often causes the generation of inactive complexes, and few techniques exist for ligating enzymes in yeast without loss of enzyme activity. Herein, we focused on sortase A, which links a short peptide tag between two target proteins. First, we demonstrated sortase A-mediated ligation in yeast using split-green fluorescent protein. Then, sortase A-mediated ligation was applied to ligate metabolic enzymes related to 3-hydroxypropionic acid, which improved 3-HP production by 2.42-fold. This strategy represents a novel approach for improving yeast bioproduction.

Klebsiella pneumoniae under xylose pressure: the growth adaptation, antimicrobial susceptibility, global proteomics analysis and role of XylA and XylB proteins

Klebsiella pneumoniae can be cultured in medium with xylose as the sole carbon source. However, the effect of xylose exposure on its growth adaptation, virulence, antimicrobial susceptibility, and proteomic response remain unclear. Here, we show that low concentrations of xylose (≤ 2%) promote the planktonic growth of three K. pneumoniae isolates (K2044, EKP19, and EKP108) in a concentration-dependent manner, while 8% xylose consistently inhibits their planktonic growth. Notably, the xylose-induced isolate K2044-8Xyl-60G, when exposed to various xylose concentrations, exhibited the longest logarithmic growth phase and the highest optical density (OD) after logarithmic growth, compared to K2044. In contrast, the xylose-induced isolates EKP19 and EKP108 did not successfully reshape growth adaptation under persistent xylose pressure compared to K2044. Additionally, while the growth adaptation of K2044-8Xyl-60G under xylose pressure was confirmed, no amino acid mutations were detected in the functional proteins of this xylose-induced isolate, suggesting that persistent xylose pressure does not cause nonsense mutations in the bacterial genome. Xylose exposure reduced the gentamicin minimum inhibitory concentration (MIC) in all three K. pneumoniae isolates (K2044, EKP108, and EKP19) and their xylose-induced derivatives. In a Galleria mellonella infection model, significantly decreased virulence was observed in the xylose-induced isolates of K2044 and EKP19. Proteomic analysis of K2044-8Xyl-60G treated with 8% xylose revealed upregulation of proteins involved in glycolysis, the pentose phosphate pathway, and transmembrane transport. We also constructed K2044-ΔxylA (with deletion of the xylA gene) and K2044-ΔxylB (with deletion of the xylB gene). Our data showed that K2044-ΔxylA exhibited enhanced planktonic growth compared to K2044 when exposed to xylose concentrations of ≥ 4%, while K2044-ΔxylB displayed significantly reduced growth capacity regardless of xylose exposure. The virulence of K2044-ΔxylA was also significantly reduced, as demonstrated by the increased survival rates in G. mellonella infection models. Additionally, xylose exposure strongly enhanced membrane depolarization in both K2044-ΔxylA and K2044-ΔxylB compared to the wild-type K2044. Proteomic analysis indicated that the deletion of xylA primarily affected functional proteins related to ribosomes, xylose transmembrane transporters and capsular polysaccharides, while the deletion of xylB impacted the expression of xylose metabolism-related proteins. In conclusion, xylose exposure can reshape the growth adaptation, virulence, and antimicrobial susceptibility of K. pneumoniae in an isolate-specific manner, with xylA playing a more critical role than xylB under high xylose concentrations.

Advances in the biological production of sugar alcohols from biomass-derived xylose

Sugar alcohols are a common class of low-calorie sweeteners. The advancement of technologies utilizing renewable resources has heightened interest in synthesizing sugar alcohols from biomass-derived xylose for cost down of process and sustainability. This review focuses on the potential of biomass-derived xylose and its effective conversion into sugar alcohols, underscoring the significance of this process in sustainable industrial applications. The two main approaches for producing sugar alcohols which include enzyme catalysis and microbial fermentation are thoroughly discussed. The microbial fermentation pathway relies on genetically engineered strains, which are modified to efficiently convert xylose into target sugar alcohols. Enzyme catalysis, on the other hand, directly converts xylose to sugar alcohols through specific reactions. In addition, strategies to improve product selectivity and reduce by-products are discussed in the paper, which are crucial for improving the economic viability and environmental sustainability of sugar alcohol production. Overall, utilizing xylose from biomass to produce sugar alcohols manifests environmental and economic benefits, indicating its substantial potential in the shift towards a low-carbon economy. Future studies may further explore cutting edge technologies to maximize the utilization of biomass-derived xylose and the sustainable production of sugar alcohols.

Carbon catabolite repression during the simultaneous utilization of lignocellulose-derived sugars in lactic acid production: Influencing factors and mitigation strategies

Lignocellulose is the most abundant, sustainable, and comparatively economical renewable biomass containing ample fermentable sugars for bio-based chemical production, such as lactic acid (LA). LA is a versatile chemical with substantial global demand. However, the concurrent utilization of mixed sugars derived from lignocellulose, including glucose, xylose, and arabinose, remains a formidable challenge because of the metabolic regulation of carbon catabolite repression (CCR), in which glucose is preferentially utilized over non-glucose sugars, resulting in the loss of carbon resources and a decrease in biorefinery efficacy. Most current studies on CCR have concentrated on elucidating the principles and their impact on specific bacterial species using mixed carbon sources. However, there remains a notable dearth of comprehensive reviews summarizing the underlying principles and corresponding mitigation strategies across other bacterial strains encountering similar challenges. In light of this, this article delineates the possible factors that lead to CCR, including signal transduction and metabolic pathways. Additionally, the fermentation conditions and nutrients are described. Finally, this study proposes appropriate mitigation strategies to overcome the aforementioned obstacles and presents new insights into the rapid and simultaneous consumption of mixed sugars to bolster the production yields of biofuels and chemicals in the future.

Engineering Saccharomyces cerevisiae for growth on xylose using an oxidative pathway

The fermentative production of valuable chemicals from lignocellulosic feedstocks has attracted considerable attention. Although Saccharomyces cerevisiae is a promising microbial host, it lacks the ability to efficiently metabolize xylose, a major component of lignocellulosic feedstocks. The xylose oxidative pathway offers advantages such as simplified metabolic regulation and fewer enzymatic steps. Specifically, the pathway involves the conversion of xylose into 2-keto-3-deoxy-xylonate, which can be channeled into two distinct pathways, the Dahms pathway and the Weimberg pathway. However, the growth of yeast on xylose as the sole carbon source through the xylose oxidative pathway has not been achieved, limiting its utilization. We successfully engineered S. cerevisiae to metabolize xylose as its sole carbon source via the xylose oxidative pathways, achieved by enhancing enzyme activities through iron metabolism engineering and rational enzyme selection. We found that increasing the supply of the iron-sulfur cluster to activate the bottleneck enzyme XylD by BOL2 disruption and tTYW1 overexpression facilitated the growth of xylose and the production of ethylene glycol at 1.5 g/L via the Dahms pathway. Furthermore, phylogenetic analysis of xylonate dehydratases led to the identification of a highly active homologous enzyme. A strain possessing the Dahms pathway with this highly active enzyme exhibited reduced xylonate accumulation. Furthermore, the introduction of enzymes based on phylogenetic tree analysis allowed for the utilization of xylose as the sole carbon source through the Weimberg pathway. This study highlights the potential of iron metabolism engineering and phylogenetic enzyme selection for the development of non-native metabolic pathways in yeast. KEY POINTS: • A 1.5 g/L ethylene glycol was produced via the Dahms pathway in S. cerevisiae. • Enzyme activation enabled growth on xylose via both the Dahms and Weimberg pathways. • Tested enzymes in this study may expand the application of xylose oxidative pathway.

Evolving Nonphosphorylative Metabolism for Improving Production of 2-Oxoglutarate Derivatives

The bioconversion of lignocellulosic biomass into value-added products provides an alternative solution to environmental and economic challenges. Nonphosphorylative metabolism can convert pentoses and d-galacturonate into 2-oxoglutarate (2-KG) in a few steps, facilitating the production of 2-KG derivatives. However, the efficiency of the Weimberg pathway from Caulobacter crescentus, a type of nonphosphorylative metabolism, is constrained by the low activity of CcXylX, 2-keto-3-deoxy-d-xylonate dehydratase. To overcome this limitation, we engineered CcXylX through directed evolution. A resulting CcXylX mutant exhibited a 3-fold higher kcat value and notably enhanced the production of 2-KG derivatives from d-xylose, a major component of lignocellulosic hydrolysates, including a 32% increase in l-glutamate titer (8.3 g/L) and a 79% increase in l-proline titer (4.3 g/L) compared with the wild-type CcXylX. This research holds promise for advancing lignocellulosic biotechnology and provides insights into economically viable production of other 2-KG derivatives besides l-glutamate and l-proline.

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

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

β-(1 → 3)(1 → 6)glucan from Schizophyllum commune 227E.32: High yield production via glucose/xylose co-metabolization

A co-metabolization of xylose and glucose by Schizophyllum commune 227E.32 wild mushroom for exopolysaccharide (EPS) production is presented. Cultivations performed with S. commune 227E.32 at different xylose concentrations demonstrated that the concentration of 50 g·L-1 of xylose achieved the highest EPS production, around 4.46 g·L-1. Scale-up in a stirred tank reactor (STR) was performed. 10 % inoculum showed the highest cost/benefit ratio regarding sugar conversion and EPS production (Y P/S = 0.90 g·g-1), achieving 1.82 g·L-1 of EPS. Isolation, purification, and characterization were conducted with EPS produced in flasks and STR. GC-MS analysis showed glucose as main monosaccharide constituents for both isolates. 13C NMR and HSQC-edited showed that both EPS isolated consisted of a β-D-Glcp (1 → 3) main chain, partially substituted at O-6 with nonreducing β-D-Glcp ends on every third residue, similar to β-D-glucan isolated from S. commune basidiomes known as schizophyllan (SPG). The Mw was determined by GPC to 1.5 × 106 Da (flasks) and 1.1 × 106 Da (STR). AFM topographs revealed a semi-flexible appearance of the β-D-glucan, consistent with the triple helical structures adopted by SPG and overall contour length consistent with a high molar mass.

Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates

Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.

Utilization of Macroalgae for the Production of Bioactive Compounds and Bioprocesses Using Microbial Biotechnology

To achieve sustainable development, alternative resources should replace conventional resources such as fossil fuels. In marine ecosystems, many macroalgae grow faster than terrestrial plants. Macroalgae are roughly classified as green, red, or brown algae based on their photosynthetic pigments. Brown algae are considered to be a source of physiologically active substances such as polyphenols. Furthermore, some macroalgae can capture approximately 10 times more carbon dioxide from the atmosphere than terrestrial plants. Therefore, they have immense potential for use in the environment. Recently, macroalgae have emerged as a biomass feedstock for bioethanol production owing to their low lignin content and applicability to biorefinery processes. Herein, we provided an overview of the bioconversion of macroalgae into bioactive substances and biofuels using microbial biotechnology, including engineered yeast designed using molecular display technology.

Unravel the regulatory mechanism of Yrr1p phosphorylation in response to vanillin stress in Saccharomyces cerevisiae

Improving the resistance of Saccharomyces cerevisiae to vanillin, derived from lignin, will benefit the design of robust cell factories for lignocellulosic biorefining. The transcription factor Yrr1p mediates S. cerevisiae resistance to various compounds. In this study, eleven predicted phosphorylation sites were mutated, among which 4 mutants of Yrr1p, Y134A/E and T185A/E could improve vanillin resistance. Both dephosphorylated and phosphorylated mutations at Yrr1p 134 and 185 gathered in the nucleus regardless of the presence or absence of vanillin. However, the phosphorylated mutant Yrr1p inhibited target gene expression, while dephosphorylated mutants promoted expression. Transcriptomic analysis showed that the dephosphorylated Yrr1p T185 mutant, under vanillin stress, upregulated ribosome biogenesis and rRNA processing. These results demonstrate the mechanism by which Yrr1p phosphorylation regulates the expression of target genes. The identification of key phosphorylation sites in Yrr1p offers novel targets for the rational construction of Yrr1p mutants to improve resistance to other compounds.

Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates

Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log₂ fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.

Rewiring of metabolic pathways in yeasts for sustainable production of biofuels

The ever-increasing global energy demand has led world towards negative repercussions such as depletion of fossil fuels, pollution, global warming and climate change. Designing microbial cell factories for the sustainable production of biofuels is therefore an active area of research. Different yeast cells have been successfully engineered using synthetic biology and metabolic engineering approaches for the production of various biofuels. In the present article, recent advancements in genetic engineering strategies for production of bioalcohols, isoprenoid-based biofuels and biodiesels in different yeast chassis designs are reviewed, along with challenges that must be overcome for efficient and high titre production of biofuels.

Bioconversion of corn fiber to bioethanol: Status and perspectives

Due to the rising demand for green energy, bioethanol has attracted increasing attention from academia and industry. Limited by the bottleneck of bioethanol yield in traditional corn starch dry milling processes, an increasing number of studies focus on fully utilizing all corn ingredients, especially kernel fiber, to further improve the bioethanol yield. This mini-review addresses the technological challenges and opportunities on the way to achieving the efficient conversion of corn fiber. Significant advances during the review period include the detailed characterization of different forms of corn kernel fiber and the development of off-line and in-situ conversion strategies. Lessons from cellulosic ethanol technologies offer new ways to utilize corn fiber in traditional processes. However, the commercialization of corn kernel fiber conversion may be hampered by enzyme cost, conversion efficiency, and overall process economics. Thus, future studies should address these technical limitations.

Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass

Xylitol dehydrogenase (XDH) catalyzes the NAD⁺-dependent oxidization of xylitol into D-xylulose, and belongs to a zinc-dependent medium-chain dehydrogenase/reductase family. This protein family consists of enzymes with one or two zinc atoms per subunit, among which catalytic zinc is necessary for the activity. Among many XDHs from yeast and fungi, XDH from Pichia stipitis is one of the key enzymes for bioethanol production by lignocellulosic biomass, and possesses only a catalytic zinc atom. Despite its importance in bioindustry, a structural data of XDH has not yet been available, and little insight into the role of a second zinc atom in this protein family is known. We herein report the crystal structure of XDH from P. stipitis using a thermostabilized mutant. In the refined structure, a second zinc atom clearly coordinated with four artificially introduced cysteine ligands. Homologous mutations in XDH from Saccharomyces cerevisiae also stabilized and enhanced activity. The substitution of each of the four cysteine ligands with an aspartate in XDH from Schizosaccharomyces pombe contributed to the significantly better maintenance of activity and thermostability than their substitution with a serine, providing a novel hypothesis for how this zinc atom was eliminated.

Fermentation of D-xylose to Ethanol by Saccharomyces cerevisiae CAT-1 Recombinant Strains

Ethanol production by the D-xylose fermentation of lignocellulosic biomass would augment environmental sustainability by increasing the yield of biofuel obtained per cultivated area. A set of recombinant strains derived from the industrial strain Saccharomyces cerevisiae CAT-1 was developed for this purpose. First, two recombinant strains were obtained by the chromosomal insertion of genes involved in the assimilation and transport of D-xylose (Gal2-N376F). Strain CAT-1-XRT was developed with heterologous genes for D-xylose metabolism from the oxo-reductive pathway of Scheffersomyces stipitis (XYL1-K270R, XYL2); and strain CAT-1-XIT, with D-xylose isomerase (xylA gene, XI) from Streptomyces coelicolor. Moreover, both recombinant strains contained extra copies of homologous genes for xylulose kinase (XK) and transaldolase (TAL1). Furthermore, plasmid (pRS42K::XI) was constructed with xylA from Piromyces sp. transferred to CAT-1, CAT-1-XRT, and CAT-1-XIT, followed by an evolution protocol. After 10 subcultures, CAT-1-XIT (pRS42K::XI) consumed 74% of D-xylose, producing 12.6 g/L ethanol (0.31 g ethanol/g D-xylose). The results of this study show that CAT-1-XIT (pRS42K::XI) is a promising recombinant strain for the efficient utilization of D-xylose to produce ethanol from lignocellulosic materials.

High-level production of xylose from agricultural wastes using GH11 endo-xylanase and GH43 β-xylosidase from Bacillus sp

As a promising feedstock, alkali-extracted xylan from lignocellulosic biomass is desired for producing xylose, which can be used for renewable biofuels production. In this study, an efficient pathway has been established for low-cost and high-yield production of xylose by hydrolysis of alkali-extracted xylan from agricultural wastes using an endo-1,4-xylanase (XYLA) from Bacillus safensis TCCC 111022 and a β-xylosidase (XYLO) from B. pumilus TCCC 11573. The optimum activities of recombinant XYLA (rXYLA) and XYLO (rXYLO) were 60 ℃ and pH 8.0, and 30 ℃ and pH 7.0, respectively. They were stable over a broad pH range (pH 6.0-11.0 and 7.0-10.0). rXYLO showed a relatively high xylose tolerance up to 100 mM. Furthermore, the yield of xylose from wheat straw, rice straw, corn stover, corncob and sugarcane bagasse by rXYLA and rXYLO was 63.77%, 71.76%, 68.55%, 53.81%, and 58.58%, respectively. This study demonstrated a strategy to produce xylose from agricultural wastes by integrating alkali-extracted xylan and enzymatic hydrolysis.

Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.

Cellulosic Ethanol Production Using a Dual Functional Novel Yeast

Reducing the cost of cellulosic ethanol production, especially for cellulose hydrolytic enzymes, is vital to growing a sustainable and efficient cellulosic ethanol industry and bio-based economy. Using an ethanologenic yeast able to produce hydrolytic enzymes, such as Clavispora NRRL Y-50464, is one solution. NRRL Y-50464 is fast-growing and robust, and tolerates inhibitory compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) associated with lignocellulose-to-fuel conversion. It produces three forms of β-glucosidase isozymes, BGL1, BGL2, and BGL3, and ferment cellobiose as the sole carbon source. These β-glucosidases exhibited desirable enzyme kinetic parameters and high levels of enzyme-specific activity toward cellobiose and many oligosaccharide substrates. They tolerate the product inhibition of glucose and ethanol, and are stable to temperature and pH conditions. These characteristics are desirable for more efficient cellulosic ethanol production by simultaneous saccharification and fermentation. NRRL Y-50464 provided the highest cellulosic ethanol titers and conversion rates at lower cellulase loadings, using either pure cellulose or agricultural residues, as so far reported in the literature. This review summarizes NRRL Y-50464 performance on cellulosic ethanol production from refined cellulose, rice straw, and corn stover processed in various ways, in the presence or absence of furfural and HMF. This dual functional yeast has potential to serve as a prototype for the development of next-generation biocatalysts. Perspectives on continued strain development and process engineering improvements for more efficient cellulosic ethanol production from lignocellulosic materials are also discussed.

Coordinately express hemicellulolytic enzymes in Kluyveromyces marxianus to improve the saccharification and ethanol production from corncobs

BACKGROUND

Hemicellulose acts as one factor contributing to the recalcitrance of lignocellulose that prevents cellulases to degrade the cellulose efficiently even in low quantities. Supplement of hemicellulases can enhance the performance of commercial cellulases in the enzymatic hydrolyses of lignocellulose. Kluyveromyce marxianus is an attractive yeast for cellulosic ethanol fermentation, as well as a promising host for heterologous protein production, since it has remarkable thermotolerance, high growth rate, and broad substrate spectrum etc. In this study, we attempted to coordinately express multiple hemicellulases in K. marxianus through a 2A-mediated ribosome skipping to self-cleave polyproteins, and investigated their capabilities for saccharification and ethanol production from corncobs.

RESULTS

Two polycistronic genes IMPX and IMPαX were constructed to test the self-cleavage of P2A sequence from the Foot-and-Mouth Disease virus (FMDV) in K. marxianus. The IMPX gene consisted of a β-mannanase gene M330 (without the stop codon), a P2A sequence and a β-xylanase gene Xyn-CDBFV in turn. In the IMPαX gene, there was an additional α-factor signal sequence in frame with the N-terminus of Xyn-CDBFV. The extracellular β-mannanase activities of the IMPX and IMPαX strains were 21.34 and 15.50 U/mL, respectively, but the extracellular β-xylanase activity of IMPαX strain was much higher than that of the IMPX strain, which was 136.17 and 42.07 U/mL, respectively. Subsequently, two recombinant strains, the IXPαR and IMPαXPαR, were constructed to coordinately and secretorily express two xylantic enzymes, Xyn-CDBFV and β-D-xylosidase RuXyn1, or three hemicellulolytic enzymes including M330, Xyn-CDBFV and RuXyn1. In fed-batch fermentation, extracellular activities of β-xylanase and β-xylosidase in the IXPαR strain were 1664.2 and 0.90 U/mL. Similarly, the IMPαXPαR strain secreted the three enzymes, β-mannanase, β-xylanase, and β-xylosidase, with the activities of 159.8, 2210.5, and 1.25 U/mL, respectively. Hemicellulolases of both strains enhanced the yields of glucose and xylose from diluted acid pretreated (DAP) corncobs when acted synergistically with commercial cellulases. In hybrid saccharification and fermentation (HSF) of DAP corncobs, hemicellulases of the IMPαXPαR strain increased the ethanol yield by 8.7% at 144 h compared with the control. However, both ethanol and xylose yields were increased by 12.7 and 18.2%, respectively, at 120 h in HSF of aqueous ammonia pretreated (AAP) corncobs with this strain. Our results indicated that coordinate expression of hemicellulolytic enzymes in K. marxianus promoted the saccharification and ethanol production from corncobs.

CONCLUSIONS

The FMDV P2A sequence showed high efficiency in self-cleavage of polyproteins in K. marxianus and could be used for secretory expression of multiple enzymes in the presence of their signal sequences. The IMPαXPαR strain coexpressed three hemicellulolytic enzymes improved the saccharification and ethanol production from corncobs, and could be used as a promising strain for ethanol production from lignocelluloses.

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.

Engineering Yarrowia lipolytica to produce fuels and chemicals from xylose: A review

The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental attractiveness. However, the utilized microorganisms must be able to use all the sugars present in lignocellulosic hydrolysates, especially xylose, the second most plentiful monosaccharide on earth. Yarrowia lipolytica is a good candidate for producing various valuable products from biomass, but this yeast is unable to catabolize xylose efficiently. The development of metabolic engineering facilitated the application of Y. lipolytica as a platform for the bioconversion of xylose into various value-added products. Here, we reviewed the research progress on natural xylose-utilization pathways and their reconstruction in Y. lipolytica. The progress and emerging trends in metabolic engineering of Y. lipolytica for producing chemicals and fuels are further introduced. Finally, challenges and future perspectives of using lignocellulosic hydrolysate as substrate for Y. lipolytica are discussed.

Characterization of a microbial consortium with potential for biological degradation of cactus pear biomass for biofuel production

Cactus pear (Opuntia ficus-indica) is a crassulacean acid metabolism (CAM) species that serves as a food, feed, and bioenergy crop. O. ficus-indica is an attractive alternative biofuel feedstock due to its low water demand and high biomass productivity. Current ethanol yields from O. ficus-indica are not commercially viable due to low concentrations of released fermentable carbohydrates. Axenic strains of bacteria and fungi were isolated and characterized from a soil microbial community consortium that effectively degrades cladodes into soluble components. The consortium consisted of species representing 14 genera of eubacteria and four genera of fungi. The digestion efficiency of each axenic isolate was evaluated by measuring the release of soluble material after aerobic digestion of cladodes and direct measurement of cellulase and pectinase activities in the culture supernatants. Pectobacterium cacticida was the most effective eubacterial species identified for degrading cladodes among all isolates evaluated. Thus, P. cacticida holds great promise for increasing the release of fermentable sugars and improving overall ethanol yields.

Understanding D-xylonic acid accumulation: a cornerstone for better metabolic engineering approaches

The xylose oxidative pathway (XOP) has been engineered in microorganisms for the production of a wide range of industrially relevant compounds. However, the performance of metabolically engineered XOP-utilizing microorganisms is typically hindered by D-xylonic acid accumulation. It acidifies the media and perturbs cell growth due to toxicity, thus curtailing enzymatic activity and target product formation. Fortunately, from the growing portfolio of genetic tools, several strategies that can be adapted for the generation of efficient microbial cell factories have been implemented to address D-xylonic acid accumulation. This review centers its discussion on the causes of D-xylonic acid accumulation and how to address it through different engineering and synthetic biology techniques with emphasis given on bacterial strains. In the first part of this review, the ability of certain microorganisms to produce and tolerate D-xylonic acid is also tackled as an important aspect in developing efficient microbial cell factories. Overall, this review could shed some insights and clarity to those working on XOP in bacteria and its engineering for the development of industrially applicable product-specialist strains. KEY POINTS: D-Xylonic acid accumulation is attributed to the overexpression of xylose dehydrogenase concomitant with basal or inefficient expression of enzymes involved in D-xylonic acid assimilation. Redox imbalance and insufficient cofactors contribute to D-xylonic acid accumulation. Overcoming D-xylonic acid accumulation can increase product formation among engineered strains. Engineering strategies involving enzyme engineering, evolutionary engineering, coutilization of different sugar substrates, and synergy of different pathways could potentially address D-xylonic acid accumulation.

Minimize the Xylitol Production in Saccharomyces cerevisiae by Balancing the Xylose Redox Metabolic Pathway

Xylose is the second most abundant sugar in lignocellulose, but it cannot be used as carbon source by budding yeast Saccharomyces cerevisiae. Rational promoter elements engineering approaches were taken for efficient xylose fermentation in budding yeast. Among promoters surveyed, HXT7 exhibited the best performance. The HXT7 promoter is suppressed in the presence of glucose and derepressed by xylose, making it a promising candidate to drive xylose metabolism. However, simple ectopic expression of both key xylose metabolic genes XYL1 and XYL2 by the HXT7 promoter resulted in massive accumulation of the xylose metabolic byproduct xylitol. Through the HXT7-driven expression of a reported redox variant, XYL1-K270R, along with optimized expression of XYL2 and the downstream pentose phosphate pathway genes, a balanced xylose metabolism toward ethanol formation was achieved. Fermented in a culture medium containing 50 g/L xylose as the sole carbon source, xylose is nearly consumed, with less than 3 g/L xylitol, and more than 16 g/L ethanol production. Hence, the combination of an inducible promoter and redox balance of the xylose utilization pathway is an attractive approach to optimizing fuel production from lignocellulose.

Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding

Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335′s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log₂ fold change (FC) >|1| and 106 highly DEGs (log₂ FC >|2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation–reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.

Conservation of Xylose Fermentability in Phlebia Species and Direct Fermentation of Xylan by Selected Fungi

In efforts to lower the cost of total conversion of lignocellulosic materials, utilization of hemicellulose must be considered. White-rot fungus Phlebia sp. MG-60 can produce ethanol directly from cellulose and has fermentation ability for glucose, cellulose, and xylose. Therefore, white-rot fungi can be considered a good candidate for consolidated bioprocessing to give bioethanol from lignocellulosic biomass, although little information is available on the direct fermentation of xylan. In the present study, some Phlebia species were selected as candidates because of their ability to ferment xylose to ethanol more efficiently than Phlebia sp. MG-60. This process indicated that the basidiomycetes that can produce ethanol from xylose are closely related genetically within the Phlebia genus. The selected Phlebia species showed higher ethanol productivity from corn core and beechwood xylans than Phlebia sp. MG-60. The ethanol yields from corn core xylan in culture with Phlebia acerina HHB11146, Phlebia ludoviciana HHB9640, and Phlebia subochracea HHB8494 were 46.2%, 46.7%, and 39.7% of theoretical maximum, and those from beechwood xylan were 19.09%, 17.7%, and 21.4% of the theoretical maximum, respectively.

Saccharomyces cerevisiae and its industrial applications

Saccharomyces cerevisiae is the best studied eukaryote and a valuable tool for most aspects of basic research on eukaryotic organisms. This is due to its unicellular nature, which often simplifies matters, offering the combination of the facts that nearly all biological functions found in eukaryotes are also present and well conserved in S. cerevisiae. In addition, it is also easily amenable to genetic manipulation. Moreover, unlike other model organisms, S. cerevisiae is concomitantly of great importance for various biotechnological applications, some of which date back to several thousands of years. S. cerevisiae's biotechnological usefulness resides in its unique biological characteristics, i.e., its fermentation capacity, accompanied by the production of alcohol and CO2 and its resilience to adverse conditions of osmolarity and low pH. Among the most prominent applications involving the use of S. cerevisiae are the ones in food, beverage -especially wine- and biofuel production industries. This review focuses exactly on the function of S. cerevisiae in these applications, alone or in conjunction with other useful microorganisms involved in these processes. Furthermore, various aspects of the potential of the reservoir of wild, environmental, S. cerevisiae isolates are examined under the perspective of their use for such applications.

Synthetic Biology Applied to Carbon Conservative and Carbon Dioxide Recycling Pathways

The global warming conjugated with our reliance to petrol derived processes and products have raised strong concern about the future of our planet, asking urgently to find sustainable substitute solutions to decrease this reliance and annihilate this climate change mainly due to excess of CO₂ emission. In this regard, the exploitation of microorganisms as microbial cell factories able to convert non-edible but renewable carbon sources into biofuels and commodity chemicals appears as an attractive solution. However, there is still a long way to go to make this solution economically viable and to introduce the use of microorganisms as one of the motor of the forthcoming bio-based economy. In this review, we address a scientific issue that must be challenged in order to improve the value of microbial organisms as cell factories. This issue is related to the capability of microbial systems to optimize carbon conservation during their metabolic processes. This initiative, which can be addressed nowadays using the advances in Synthetic Biology, should lead to an increase in products yield per carbon assimilated which is a key performance indice in biotechnological processes, as well as to indirectly contribute to a reduction of CO₂ emission.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.

Protein adaptors assemble functional proteins on DNA scaffolds

DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.

Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose

BACKGROUND

Aromatic amino acids and their derivatives are valuable chemicals and are precursors for different industrially compounds. p-Coumaric acid is the main building block for complex secondary metabolites in commercial demand, such as flavonoids and polyphenols. Industrial scale production of this compound from yeast however remains challenging.

RESULTS

Using metabolic engineering and a systems biology approach, we developed a Saccharomyces cerevisiae platform strain able to produce 242 mg/L of p-coumaric acid from xylose. The same strain produced only 5.35 mg/L when cultivated with glucose as carbon source. To characterise this platform strain further, transcriptomic analysis was performed, comparing this strain's growth on xylose and glucose, revealing a strong up-regulation of the glyoxylate pathway alongside increased cell wall biosynthesis and unexpectedly a decrease in aromatic amino acid gene expression when xylose was used as carbon source.

CONCLUSIONS

The resulting S. cerevisiae strain represents a promising platform host for future production of p-coumaric using xylose as a carbon source.

Promoter engineering strategies for the overproduction of valuable metabolites in microbes

Promoter engineering is an enabling technology in metabolic engineering and synthetic biology. As an indispensable part of synthetic biology, the promoter is a key factor in regulating genetic circuits and in coordinating multi-gene biosynthetic pathways. In this review, we summarized the recent progresses in promoter engineering in microbes. Specifically, the endogenous promoters are firstly discussed, followed by the statement of the influence of nucleotides exchange on the strength of promoters explored by site-selective mutagenesis. We then introduced the promoter libraries with a wide range of strength, which are constructed focusing on core promoter regions and upstream activating sequences by rational designs. Finally, the application of promoter libraries in the optimization of multi-gene metabolic pathways for high-yield production of metabolites was illustrated with a couple of recent examples.

Understanding xylose isomerase from Burkholderia cenocepacia: insights into structure and functionality for ethanol production

The inability of the yeast Saccharomyces cerevisiae to produce ethanol from xylose has hampered the biofuel production from lignocellulosic biomass. However, prior studies reveal that functional expression of xylose isomerase (XI) from Burkholderia cenocepacia (XylA_Bc) in S. cerevisiae has remarkably improved xylose consumption and ethanol productivity. Yet, little is known about kinetic and structural properties of this enzyme. Hereby, a purified recombinant XylA was assayed in vitro, showing optimal enzyme activity at 37 °C and pH 7.2. The K_m of XylA for d-xylose was at least threefold lower than the K_m results for any XI published to date (e.g. XylA from Piromyces sp.). In addition, oligomerization behavior as a tetramer was observed for XylA in solution. Functional and structural comparative analyses amongst three microbial XIs were further performed as theoretical models, showing that xylose orientation at the active site was highly conserved among the XIs. Mg²⁺ ions anchor the sugar and guide its pyranoside oxygen towards a histidine residue present at the active site, allowing an acid–base reaction, linearizing xylose. Electrostatic surface analyses showed that small variations in the net charge distribution and dipole moment could directly affect the way the substrate interacts with the protein, thus altering its kinetic properties. Accordingly, in silico modeling suggested the tetramer may be the major functional form. These analyses and the resulting model promote a better understanding of this protein family and pave the way to further protein engineering and application of XylA in the ethanol industry.

Modular Engineering of Biomass Degradation Pathways

Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.

Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis

Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 Å resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.

Engineering Saccharomyces cerevisiae for Enhanced Production of Protopanaxadiol with Cofermentation of Glucose and Xylose

Protopanaxadiol (PPD), an active triterpene compound, is the precursor of high-value ginsenosides. In this study, we report a strategy for the enhancement of PPD production in Saccharomyces cerevisiae by cofermentation of glucose and xylose. In mixed sugar fermentation, strain GW6 showed higher PPD titer and yield than that obtained from glucose cultivation. Then, engineering strategies were implemented on GW6 to enhance the PPD yields, such as adjustment of the central carbon metabolism, optimization of the mevalonate pathway, reinforcement of the xylose assimilation pathway, and regulation of cofactor balance, namely, overexpression of xPK/PTA, ERG10/ERG12/ERG13, XYL1/XYL2/TAL1, and POS5, respectively. In particular, the final obtained strain GW10, harboring overexpressed POS5, exhibited the highest PPD yield, which was 2.06 mg of PPD/g of mixed sugar. In a 5-L fermenter, PPD titer reached 152.37 mg/L. These promising results demonstrate the great advantages of mixed sugar over glucose for high-yield production of PPD.

Improved xylose tolerance and 2,3-butanediol production of Klebsiella pneumoniae by directed evolution of rpoD and the mechanisms revealed by transcriptomics

BACKGROUND

The biological production of 2,3-butanediol from xylose-rich raw materials from Klebsiella pneumoniae is a low-cost process. RpoD, an encoding gene of the sigma factor, is the key element in global transcription machinery engineering and has been successfully used to improve the fermentation with Escherichia coli. However, whether it can regulate the tolerance in K. pneumoniae remains unclear.

RESULTS

In this study, the kpC mutant strain was constructed by altering the expression quantity and genotype of the rpoD gene, and this exhibited high xylose tolerance and 2,3-butanediol production. The xylose tolerance of kpC strain was increased from 75 to 125 g/L, and the yield of 2,3-butanediol increased by 228.5% compared with the parent strain kpG, reaching 38.6 g/L at 62 h. The RNA sequencing results showed an upregulated expression level of 500 genes and downregulated expression level of 174 genes in the kpC mutant strain. The pathway analysis further showed that the differentially expressed genes were mainly related to signal transduction, membrane transport, carbohydrate metabolism, and energy metabolism. The nine most-promising genes were selected based on transcriptome sequencing, and were evaluated for their effects on xylose tolerance. The overexpression of the tktA encoding transketolase, pntA encoding NAD(P) transhydrogenase subunit alpha, and nuoF encoding NADH dehydrogenase subunit F conferred increased xylose consumption and increased 2,3-butanediol production to K. pneumoniae.

CONCLUSIONS

These results suggest that the xylose tolerance and 2,3-butanediol production of K. pneumoniae can be greatly improved by the directed evolution of rpoD. By applying transcriptomic analysis, the upregulation of tktA, pntA, and nuoF that were coded are essential for the xylose consumption and 2,3-butanediol production. This study will provide reference for further research on improving the fermentation abilities by means of other organisms.