A novel method to prepare L-arabinose from xylose mother liquor by yeast-mediated biopurification

A Novel Bio-Purification Process Employing an Engineered E. coli Strain for Downstream Processing of Lactic Acid Solutions from the Fermentation of Agro-Industrial by-Products

This study aims to integrate a novel bio-purification process employing an engineered E. coli strain in the downstream processing of lactic acid (LA) fermentation broths from low-cost renewable biological feedstocks. Fermentation broth of candy waste and digestate mixture was used as a real biological feedstock. An engineered E. coli strain that selectively catabolize impurities without catabolizing LA was initially adapted on the biological feedstock, followed by shake flask experiments to prove the bio-purification concept. Scale-up and validation in a bench-scale bioreactor followed, before developing a semi-continuous membrane bioreactor (MBR) bio-purification process. The MBR bio-purification was assessed with biological feedstocks which simulated ultrafiltration or nanofiltration permeates. Incomplete removal of impurities and increased fouling was observed in the case of the ultrafiltration permeate. Contrarily, the nanofiltration permeate was successfully treated with MBR bio-purification, since low membrane fouling, 100% maltose and acetic acid removal, and no LA catabolism was achieved. MBR bio-purification as a post-treatment step in the downstream processing of LA was demonstrated as a promising technology for increasing the purity of LA solutions.

The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp

Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca²⁺ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.

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.

Nanofiltration for separation and purification of saccharides from biomass

Saccharide production is critical to the development of biotechnology in the field of food and biofuel. The extraction of saccharide from biomass-based hydrolysate mixtures has become a trend due to low cost and abundant biomass reserves. Compared to conventional methods of fractionation and recovery of saccharides, nanofiltration (NF) has received considerable attention in recent decades because of its high selectivity and low energy consumption and environmental impact. In this review the advantages and challenges of NF based technology in the separation of saccharides are critically evaluated. Hybrid membrane processes, i.e., combining NF with ultrafiltration, can complement each other to provide an efficient approach for removal of unwanted solutes to obtain higher purity saccharides. However, use of NF membrane separation technology is limited due to irreversible membrane fouling that results in high capital and operating costs. Future development of NF membrane technology should therefore focus on improving material stability, antifouling ability and saccharide targeting selectivity, as well as on engineering aspects such as process optimisation and membrane module design.

Yarrowia lipolytica as an emerging biotechnological chassis for functional sugars biosynthesis

Functional sugars have unique structural and physiological characteristics with applied perspectives for modern biomedical and biotechnological sectors, such as biomedicine, pharmaceutical, cosmeceuticals, green chemistry, and agro-food. They can also be used as starting matrices to produce biologically active metabolites of interests. Though numerous chemical synthesis routes have been proposed and deployed for the synthesis of rare sugars, however, many of them are limited and economically incompetent because of expensive raw starting feedstocks. Whereas, the biosynthesis by enzymatic means are often associated with high catalyst costs and low space-time yields. Microbial production of rare sugars via green routes using bio-renewable resources offers noteworthy solutions to overcome the aforementioned limitations of synthetic and enzymatic synthesis routes. From the microbial-based synthesis perspective, the lipogenic yeast Yarrowia lipolytica is rapidly evolving as the most prevalent and unique "non-model organism" in the bio-production arena. Due to high flux tendency through the tri-carboxylic acid cycle intermediates and precursors such as acetyl-CoA and malonyl-CoA, this yeast has been widely investigated to meet the increasing demand of industrially relevant fine chemicals, including functional sugars. Incredible interest in Y. lipolytica originates from its robust tolerance to unstable pH, salt levels, and organic compounds, which subsequently enable easy bioprocess optimization. Meaningfully, GRAS (generally recognized as safe) status creates Y. lipolytica as an attractive and environmentally friendly microbial host for the manufacturing of nutraceuticals, fermented food, and dietary supplements. In this review, we highlight the recent and state-of-the-art research progress on Y. lipolytica as a host to synthesize bio-based compounds of interest beyond the realm of well-known fatty acid production. The unique physicochemical properties, biotechnological applications, and biosynthesis of an array of value-added functional sugars including erythritol, threitol, fructooligosaccharides, galactooligosaccharides, isomalto-oligosaccharides, isomaltulose, trehalose, erythrulose, xylitol, and mannitol using sustainable carbon sources are thoroughly vetted. Finally, we conclude with perspectives that would be helpful to engineer Y. lipolytica in greening the twenty-first century biomedical and biotechnological sectors of the modern world.

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.

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

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

Sustainable production and biomedical application of polymalic acid from renewable biomass and food processing wastes

Polymalic acid (PMA), a homopolymer of L-malic acid (MA) generated from a yeast-like fungus Aureobasidium pullulans, has unique properties and many applications in food, biomedical, and environmental fields. Acid hydrolysis of PMA, releasing the monomer MA, has become a novel process for the production of bio-based MA, which currently is produced by chemical synthesis using petroleum-derived feedstocks. Recently, current researches attempted to develop economically competitive process for PMA and MA production from renewable biomass feedstocks. Compared to lignocellulosic biomass, PMA and MA production from low-value food processing wastes or by-products, generated from corn, sugarcane, or soybean refinery industries, showed more economical and sustainable for developing a MA derivatives platform from biomass biorefinery to chemical conversion. In the review, we compared the process feasibility for PMA fermentation with lignocellulosic biomass and food process wastes. Some useful strategies for metabolic engineering are summarized. Its changeable applicability and future prospects in food and biomedical fields are also discussed.

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.

Highly Efficient Erythritol Recovery from Waste Erythritol Mother Liquor by a Yeast-Mediated Biorefinery Process

Erythritol, a natural sugar alcohol, is produced industrially by fermentation and crystallization, but this process leaves a large amount of waste erythritol mother liquor (WEML) which contains more than 200 g/L erythritol as well as other polyol byproducts. These impurities make it very difficult to crystallize more erythritol. In our study, an efficient process for the recovery of erythritol from the WEML is described. The polyol impurities were first identified by high-performance liquid chromatography and gas chromatography-mass spectrometry, and a yeast strain Candida maltosa CGMCC 7323 was then isolated to metabolize those impurities to purify erythritol. Our results demonstrated that the process could remarkably improve the purity of erythritol and thus make the subsequent crystallization easier. This newly developed strategy is expected to have advantages in WEML treatment and provide helpful information with regard to green cell factories and zero-waste processing.

Raman and infrared spectroscopy of carbohydrates: A review

Carbohydrates are widespread and naturally occurring compounds, and essential constituents for living organisms. They are quite often reported when biological systems are studied and their role is discussed. However surprisingly, up till now there is no database collecting vibrational spectra of carbohydrates and their assignment, as has been done already for other biomolecules. So, this paper serves as a comprehensive review, where for selected 14 carbohydrates in the solid state both FT-Raman and ATR FT-IR spectra were collected and assigned. Carbohydrates can be divided into four chemical groups and in the same way is organized this review. First, the smallest molecules are discussed, i.e. monosaccharides (d-(-)-ribose, 2-deoxy-d-ribose, l-(-)-arabinose, d-(+)-xylose, d-(+)-glucose, d-(+)-galactose and d-(-)-fructose) and disaccharides (d-(+)-sucrose, d-(+)-maltose and d-(+)-lactose), and then more complex ones, i.e. trisaccharides (d-(+)-raffinose) and polysaccharides (amylopectin, amylose, glycogen). Both Raman and IR spectra were collected in the whole spectral range and discussed looking at the specific regions, i.e. region V (3600-3050cm^-1), IV (3050-2800cm^-1) and II (1200-800cm^-1) assigned to the stretching vibrations of the OH, CH/CH₂ and C-O/C-C groups, respectively, and region III (1500-1200cm^-1) and I (800-100cm^-1) dominated by deformational modes of the CH/CH₂ and CCO groups, respectively. In spite of the fact that vibrational spectra of saccharides are significantly less specific than spectra of other biomolecules (e.g. lipids or proteins), marker bands of the studied molecules can be identified and correlated with their structure.

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.

Development of bio-based fine chemical production through synthetic bioengineering

Fine chemicals that are physiologically active, such as pharmaceuticals, cosmetics, nutritional supplements, flavoring agents as well as additives for foods, feed, and fertilizer are produced by enzymatically or through microbial fermentation. The identification of enzymes that catalyze the target reaction makes possible the enzymatic synthesis of the desired fine chemical. The genes encoding these enzymes are then introduced into suitable microbial hosts that are cultured with inexpensive, naturally abundant carbon sources, and other nutrients. Metabolic engineering create efficient microbial cell factories for producing chemicals at higher yields. Molecular genetic techniques are then used to optimize metabolic pathways of genetically and metabolically well-characterized hosts. Synthetic bioengineering represents a novel approach to employ a combination of computer simulation and metabolic analysis to design artificial metabolic pathways suitable for mass production of target chemicals in host strains. In the present review, we summarize recent studies on bio-based fine chemical production and assess the potential of synthetic bioengineering for further improving their productivity.

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.

L-Arabinose isomerase and its use for biotechnological production of rare sugars

L-Arabinose isomerase (AI), a key enzyme in the microbial pentose phosphate pathway, has been regarded as an important biological catalyst in rare sugar production. This enzyme could isomerize L-arabinose into L-ribulose, as well as D-galactose into D-tagatose. Both the two monosaccharides show excellent commercial values in food and pharmaceutical industries. With the identification of novel AI family members, some of them have exhibited remarkable potential in industrial applications. The biological production processes for D-tagatose and L-ribose (or L-ribulose) using AI have been developed and improved in recent years. Meanwhile, protein engineering techniques involving rational design has effectively enhanced the catalytic properties of various AIs. Moreover, the crystal structure of AI has been disclosed, which sheds light on the understanding of AI structure and catalytic mechanism at molecular levels. This article reports recent developments in (i) novel AI screening, (ii) AI-mediated rare sugar production processes, (iii) molecular modification of AI, and (iv) structural biology study of AI. Based on previous reports, an analysis of the future development has also been initiated.

Improvement of antibiotic activity of Xenorhabdus bovienii by medium optimization using response surface methodology

Background

The production of secondary metabolites with antibiotic properties is a common characteristic to entomopathogenic bacteria Xenorhabdus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities with medicinal and agricultural interests such as antibiotic, antimycotic and insecticidal, nematicidal and antiulcer, antineoplastic and antiviral. It has been known that cultivation parameters are critical to the secondary metabolites produced by microorganisms. Even small changes in the culture medium may not only impact the quantity of certain compounds but also the general metabolic profile of microorganisms. Manipulating nutritional or environmental factors can promote the biosynthesis of secondary metabolites and thus facilitate the discovery of new natural products. This work was conducted to evaluate the influence of nutrition on the antibiotic production of X. bovienii YL002 and to optimize the medium to maximize its antibiotic production.

Results

Nutrition has high influence on the antibiotic production of X. bovienii YL002. Glycerol and soytone were identified as the best carbon and nitrogen sources that significantly affected the antibiotic production using one-factor-at-a-time approach. Response surface methodology (RSM) was applied to optimize the medium constituents (glycerol, soytone and minerals) for the antibiotic production of X. bovienii YL002. Higher antibiotic activity (337.5 U/mL) was obtained after optimization. The optimal levels of medium components were (g/L): glycerol 6.90, soytone 25.17, MgSO₄·7H₂O 1.57, (NH₄)₂SO₄ 2.55, KH₂PO₄ 0.87, K₂HPO₄ 1.11 and Na₂SO₄ 1.81. An overall of 37.8% increase in the antibiotic activity of X. bovienii YL002 was obtained compared with that of the original medium.

Conclusions

To the best of our knowledge, there are no reports on antibiotic production of X. boviebii by medium optimization using RSM. The results strongly support the use of RSM for medium optimization. The optimized medium not only resulted in a 37.8% increase of antibiotic activity, but also reduced the numbers of experiments. The chosen method of medium optimization was efficient, simple and less time consuming. This work will be useful for the development of X. bovienii cultivation process for efficient antibiotic production on a large scale, and for the development of more advanced control strategies on plant diseases.