Improvement of solvent production from xylose mother liquor by engineering the xylose metabolic pathway in Clostridium acetobutylicum EA 2018

Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development

Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.

Stepwise metabolic engineering of Candida tropicalis for efficient xylitol production from xylose mother liquor

Background

Commercial xylose purification produces xylose mother liquor (XML) as a major byproduct, which has become an inexpensive and abundant carbon source. A portion of this XML has been used to produce low-value-added products such as caramel but the remainder often ends up as an organic pollutant. This has become an issue of industrial concern. In this study, a uracil-deficient Candida tropicalis strain was engineered to efficiently convert XML to the commercially useful product xylitol.

Results

The xylitol dehydrogenase gene was deleted to block the conversion of xylitol to xylulose. Then, an NADPH regeneration system was added through heterologous expression of the Yarrowia lipolytica genes encoding 6-phosphate-gluconic acid dehydrogenase and 6-phosphate-glucose dehydrogenase. After process optimization, the engineered strain, C. tropicalis XZX-B4ZG, produced 97.10 g L^− 1 xylitol in 120 h from 300 g L^− 1 XML in a 5-L fermenter. The xylitol production rate was 0.82 g L^− 1 h^− 1 and the conversion rate was 92.40 %.

Conclusions

In conclusion, this study performed a combination of metabolic engineering and process optimizing in C. tropicalis to enhance xylitol production from XML. The use of C. tropicalis XZX-B4ZG, therefore, provided a convenient method to transform the industrial by-product XML into the useful material xylitol.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01596-1.

Bio-purification of sugar industry wastewater and production of high-value industrial products with a zero-waste concept

In recent years, biorefinery approach with a zero-waste concept has gained a lot research impetus to boost the environment and bioeconomy in a sustainable manner. The wastewater from sugar industries contains miscellaneous compounds and need to be treated chemically or biologically before being discharged into water bodies. Efficient utilization of wastewater produced by sugar industries is a key point to improve its economy. Thus, interest in the sugar industry wastes has grown in both fundamental and applied research fields, over the years. Although, traditional methods being used to process such wastewaters are effective yet are tedious, laborious and time intensive. Considering the diverse nature of wastewaters from various sugar-manufacturing processes, the development of robust, cost-competitive, sustainable and clean technologies has become a challenging task. Under the recent scenario of cleaner production and consumption, the biorefinery and/or close-loop concept, though using different technologies and multi-step processes, namely, bio-reduction, bio-accumulation or biosorption using a variety of microbial strains, has stepped-up as the method of choice for a sustainable exploitation of a wide range of organic waste matter along with the production of high-value products of industrial interests. This review comprehensively describes the use of various microbial strains employed for eliminating the environmental pollutants from sugar industry wastewater. Moreover, the main research gaps are also critically discussed along with the prospects for the efficient purification of sugar industry wastewaters with the concomitant production of high-value products using a biorefinery approach. In this review, we emphasized that the biotransformation/biopurification of sugar industry waste into an array of value-added compounds such as succinic acid, L-arabinose, solvents, and xylitol is a need of hour and is futuristic approach toward achieving cleaner production and consumption.

Metabolic Engineering and Adaptive Evolution of Clostridium beijerinckii To Increase Solvent Production from Corn Stover Hydrolysate

The production of acetone-butanol-ethanol by solventogenic Clostridium using lignocellulosic biomass can be a potential alternative to petroleum-based butanol. However, previous studies on nondetoxified lignocellulose hydrolysate could not provide better results when compared to those in synthetic medium. In this study, we engineered the pentose pathway of Clostridium beijerinckii NCIMB 8052, which was then subjected to adaptive laboratory evolution in the gradient mixture of synthetic medium and pretreated corn stover enzymatic hydrolysate (CSH) prepared according to the National Renewable Energy Laboratory (NREL) standard. The final resultant strain CIBTS1274A produced 20.7 g/L of total solvents in NREL CSH diluted to 6% initial total sugars, supplemented with ammonium acetate. This performance was comparable with that of corn-based butanol. In addition, this strain was successfully used in the scale-up operation using nondetoxified corn stover and corncob hydrolysate at Lignicell Refining Biotechnologies Ltd., which once was the only commercial biobutanol industry in the world.

Immobilization of recombinant Escherichia coli whole cells harboring xylose reductase and glucose dehydrogenase for xylitol production from xylose mother liquor

In this study, recombinant E. coli BL21(DE3)/pCDFDuet-1-XR-GDH harboring xylose reductase (XR) and glucose dehydrogenase (GDH) were immobilized and applied for the production of xylitol from xylose mother liquor (XML). Various immobilization methods were screened and the cross-linking approach with diatomite and polyetherimide as the raw materials and glutaraldehyde as the cross-linking agent was the optimal one, and the recovery activity reached of 80.3% after immobilization. The half-life of immobilized cells was 1.52 times to that of free cells. Batch experiments showed that the enzyme activity of immobilized cells remained 70.5% of the initial activity after 10 batches and the space-time yield of xylitol reached of 11.5 g/(L h). The production of xylitol from xylose mother liquor by immobilized E. coli cells containing xylose reductase and glucose dehydrogenase was reported for the first time, which paved a foundation for industrial production of xylitol from waste xylose mother liquor.

Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum

Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.

Ferric iron and extracellular electron shuttling increase xylose utilization and butanol production during fermentation with multiple solventogenic bacteria

Xylose is the second most abundant sugar derived from lignocellulose; it is considered less desirable than glucose for fermentation, and strategies that specifically increase xylose utilization in wild-type cells are goals for biofuel production. Xylose consumption, butanol production, and hydrogen production increased in both Clostridium beijerinckii and a novel solventogenic bacterium (strain DC-1) when anthraquinone-2,6,-disulfonate (AQDS) or riboflavin were used as redox mediators to transfer electrons to poorly crystalline Fe(OH)₃ as an extracellular electron sink. Strain DC-1 was most closely related to Rhizobiales bacterium Mfc52 based on 95% 16S rRNA gene sequence similarity, which demonstrates that this response is not limited to a single genus of xylose-fermenting bacteria. Xylose utilization and butanol production were negligible in control incubations containing cells plus 3% (w/v) xylose alone during a 10-day batch fermentation, for both strains tested (n-butanol titers of 0.05 g L^-1). Micromolar concentrations of AQDS and riboflavin were added as electron shuttling compounds with poorly crystalline Fe(OH)₃ as an insoluble electron acceptor, and respective n-butanol titers increased to 6.35 and 7.46 g L^-1. Increases in xylose consumption for the iron treatments were relatively high, from less than 0.49 g L^-1 (xylose alone, no iron or electron shuttling molecules) to 25.98 and 29.15 g L^-1 for the AQDS and riboflavin treatments, respectively. Hydrogen production was also 3.68 times greater for the AQDS treatment and 5.27 greater for the riboflavin treatment relative to controls. Strain DC-1 data were similar, again indicating that the effects are not specific to the genus Clostridium.

Two-step economical welan gum production by Sphingomonas sp. HT-1 from sugar industrial by-products

A two-step fermentation strategy using glucose mother liquor (GML) for cell growth and xylose mother liquor (XML) for welan gum synthesis was used to alleviate uneconomic welan gum fermentation. This study revealed: (1) optimal initial GML concentration was 11.7g/L (10g/L sugars contained); (2) optimal XML feeding strategy was pseudo-exponential fed-batch and feeding time was 12thh-54thh, amounting to 25.7g/L XML (20g/L sugars contained); and (3) in a 7.5-L bioreactor, welan gum concentration was 22.68±0.50g/L and its yield reached 0.756g/g sugars with trace residual sugars. Compared with the cost of batch fermentation using glucose as sole carbon source, the final carbon source costs decreased by 61.40% and the welan gum yield increased by 50%. GML and XML can be used as inexpensive carbon sources for welan gum production with higher yield, giving them industrial application potential to produce value-added chemicals.

ATP-Based Ratio Regulation of Glucose and Xylose Improved Succinate Production

We previously engineered E. coli YL104H to efficiently produce succinate from glucose. Furthermore, the present study proved that YL104H could also co-utilize xylose and glucose for succinate production. However, anaerobic succinate accumulation using xylose as the sole carbon source failed, probably because of an insufficient supply of energy. By analyzing the ATP generation under anaerobic conditions in the presence of glucose or xylose, we indicated that succinate production was affected by the intracellular ATP level, which can be simply regulated by the substrate ratio of xylose to glucose. This finding was confirmed by succinate production using an artificial mixture containing different xylose to glucose ratios. Using xylose mother liquor, a waste containing both glucose and xylose derived from xylitol production, a final succinate titer of 61.66 g/L with an overall productivity of 0.95 g/L/h was achieved, indicating that the regulation of the intracellular ATP level may be a useful and efficient strategy for succinate production and can be extended to other anaerobic processes.

Improving the performance of solventogenic clostridia by reinforcing the biotin synthetic pathway

An efficient production process is important for industrial microorganisms. The cellular efficiency of solventogenic clostridia, a group of anaerobes capable of producing a wealth of bulk chemicals and biofuels, must be improved for competitive commercialization. Here, using Clostridium acetobutylicum, a species of solventogenic clostridia, we revealed that the insufficient biosynthesis of biotin, a pivotal coenzyme for many important biological processes, is a major limiting bottleneck in this anaerobe's performance. To address this problem, we strengthened the biotin synthesis of C. acetobutylicum by overexpressing four relevant genes involved in biotin transport and biosynthesis. This strategy led to faster growth and improved the titer and productivity of acetone, butanol and ethanol (ABE solvents) of C. acetobutylicum in both biotin-containing and biotin-free media. Expressionally modulating these four genes by modifying the ribosome binding site further promoted cellular performance, achieving ABE solvent titer and productivity as high as 21.9g/L and 0.30g/L/h, respectively, in biotin-free medium; these values exceeded those of the wild-type strain by over 30%. More importantly, biotin synthesis reinforcement also conferred improved ability of C. acetobutylicum to use hexose and pentose sugars, further demonstrating the potential of this metabolic-engineering strategy in solventogenic clostridia.

Sugar uptake by the solventogenic clostridia

The acetone–butanol–ethanol fermentation of solventogenic clostridia was operated as a successful, worldwide industrial process during the first half of the twentieth century, but went into decline for economic reasons. The recent resurgence in interest in the fermentation has been due principally to the recognised potential of butanol as a biofuel, and development of reliable molecular tools has encouraged realistic prospects of bacterial strains being engineered to optimise fermentation performance. In order to minimise costs, emphasis is being placed on waste feedstock streams containing a range of fermentable carbohydrates. It is therefore important to develop a detailed understanding of the mechanisms of carbohydrate uptake so that effective engineering strategies can be identified. This review surveys present knowledge of sugar uptake and its control in solventogenic clostridia. The major mechanism of sugar uptake is the PEP-dependent phosphotransferase system (PTS), which both transports and phosphorylates its sugar substrates and plays a central role in metabolic regulation. Clostridial genome sequences have indicated the presence of numerous phosphotransferase systems for uptake of hexose sugars, hexose derivatives and disaccharides. On the other hand, uptake of sugars such as pentoses occurs via non-PTS mechanisms. Progress in characterization of clostridial sugar transporters and manipulation of control mechanisms to optimise sugar fermentation is described.

Transcriptional analysis of micronutrient zinc-associated response for enhanced carbohydrate utilization and earlier solventogenesis in Clostridium acetobutylicum

The micronutrient zinc plays vital roles in ABE fermentation by Clostridium acetobutylicum. In order to elucidate the zinc-associated response for enhanced glucose utilization and earlier solventogenesis, transcriptional analysis was performed on cells grown in glucose medium at the exponential growth phase of 16 h without/with supplementary zinc. Correspondingly, the gene glcG (CAC0570) encoding a glucose-specific PTS was significantly upregulated accompanied with the other two genes CAC1353 and CAC1354 for glucose transport in the presence of zinc. Additionally, genes involved in the metabolisms of six other carbohydrates (maltose, cellobiose, fructose, mannose, xylose and arabinose) were differentially expressed, indicating that the regulatory effect of micronutrient zinc is carbohydrate-specific with respects to the improved/inhibited carbohydrate utilization. More importantly, multiple genes responsible for glycolysis (glcK and pykA), acidogenesis (thlA, crt, etfA, etfB and bcd) and solventogenesis (ctfB and bdhA) of C. acetobutylicum prominently responded to the supplementary zinc at differential expression levels. Comparative analysis of intracellular metabolites revealed that the branch node intermediates such as acetyl-CoA, acetoacetyl-CoA, butyl-CoA, and reducing power NADH remained relatively lower whereas more ATP was generated due to enhanced glycolysis pathway and earlier initiation of solventogenesis, suggesting that the micronutrient zinc-associated response for the selected intracellular metabolisms is significantly pleiotropic.

Succinic acid production from xylose mother liquor by recombinant Escherichia coli strain

Succinic acid (1,4-butanedioic acid) is identified as one of important building-block chemicals. Xylose mother liquor is an abundant industrial residue in xylitol biorefining industry. In this study, xylose mother liquor was utilized to produce succinic acid by recombinant Escherichia coli strain SD121, and the response surface methodology was used to optimize the fermentation media. The optimal conditions of succinic acid fermentation were as follows: 82.62 g L⁻¹ total initial sugars, 42.27 g L⁻¹ MgCO₃ and 17.84 g L⁻¹ yeast extract. The maximum production of succinic acid was 52.09 ± 0.21 g L⁻¹ after 84 h with a yield of 0.63 ± 0.03 g g⁻¹ total sugar, approaching the predicted value (53.18 g L⁻¹). It was 1.78-fold of the production of that obtained with the basic medium. This was the first report on succinic acid production from xylose mother liquor by recombinant E. coli strains with media optimization using response surface methodology. This work suggested that the xylose mother liquor could be an alternative substrate for the economical production of succinic acid by recombinant E. coli strains.