The industrial versatility of Gluconobacter oxydans: current applications and future perspectives

Continuous catalytic production of 1,3-dihydroxyacetone: Sustainable approach combining perfusion cultures and immobilized cells

Currently, the predominant method for the industrial production of 1,3-dihydroxyacetone (DHA) from glycerol involves fed-batch fermentation. However, previous research has revealed that in the biocatalytic synthesis of DHA from glycerol, when the DHA concentration exceeded 50 g·L-1, it significantly inhibited microbial growth and metabolism, posing a challenge in maintaining prolonged and efficient catalytic production of DHA. In this study, a new integrated continuous production and synchronous separation (ICSS) system was constructed using hollow fiber columns and perfusion culture technology. Additionally, a cell reactivation technique was implemented to extend the biocatalytic ability of cells. Compared with fed-batch fermentation, the ICSS system operated for 360 h, yielding a total DHA of 1237.8 ± 15.8 g. The glycerol conversion rate reached 97.7 %, with a productivity of 3.44 g·L-1·h-1, representing 485.0 % increase in DHA production. ICSS system exhibited strong operational characteristics and excellent performance, indicating significant potential for applications in industrial bioprocesses.

Deciphering styrene oxide tolerance mechanisms in Gluconobacter oxydans mutant strain

Chemical production wastewater contains large amounts of organic solvents (OSs), which pose a significant threat to the environment. In this study, a 10 g·L-1 styrene oxide tolerant strain with broad-spectrum OSs tolerance was obtained via adaptive laboratory evolution. The mechanisms underlying the high OS tolerance of tolerant strain were investigated by integrating physiological, multi-omics, and genetic engineering analyses. Physiological changes are one of the main factors responsible for the high OS tolerance in mutant strains. Moreover, the P-type ATPase GOX_RS04415 and the LysR family transcriptional regulator GOX_RS04700 were also verified as critical genes for styrene oxide tolerance. The tolerance mechanisms of OSs can be used in biocatalytic chassis cell factories to synthesize compounds and degrade environmental pollutants. This study provides new insights into the mechanisms underlying the toxicological response to OS stress and offers potential targets for enhancing the solvent tolerance of G. oxydans.

CRISPR/Cpf1-FOKI-induced gene editing in Gluconobacter oxydans

Gluconobacter oxydans is an important Gram-negative industrial microorganism that produces vitamin C and other products due to its efficient membrane-bound dehydrogenase system. Its incomplete oxidation system has many crucial industrial applications. However, it also leads to slow growth and low biomass, requiring further metabolic modification for balancing the cell growth and incomplete oxidation process. As a non-model strain, G. oxydans lacks efficient genome editing tools and cannot perform rapid multi-gene editing and complex metabolic network regulation. In the last 15 years, our laboratory attempted to deploy multiple CRISPR/Cas systems in different G. oxydans strains and found none of them as functional. In this study, Cpf1-based or dCpf1-based CRISPRi was constructed to explore the targeted binding ability of Cpf1, while Cpf1-FokI was deployed to study its nuclease activity. A study on Cpf1 found that the CRISPR/Cpf1 system could locate the target genes in G. oxydans but lacked the nuclease cleavage activity. Therefore, the CRISPR/Cpf1-FokI system based on FokI nuclease was constructed. Single-gene knockout with efficiency up to 100% and double-gene iterative editing were achieved in G. oxydans. Using this system, AcrVA6, the anti-CRISPR protein of G. oxydans was discovered for the first time, and efficient genome editing was realized.

Metagenomic, organoleptic profiling, and nutritional properties of fermented kombucha tea substituted with recycled substrates

Kombucha fermentation yields a diverse range of beneficial macro and micronutrients. In our study, we examined the metabolites, antioxidant activity, organoleptic characteristics, and nutritional attributes of traditionally prepared kombucha tea, using black tea and sugar (control) as substrates, and compared them with tea made from tea dust and blackstrap molasses (test). Kombucha tea crafted from functional raw materials exhibited enhanced sensory qualities and improved health-promoting properties. The levels of tannins, flavonoids, and phenols play a crucial role in determining the antioxidant activity of kombucha tea. Using the DPPH and FRAP methods, we investigated the antioxidant activity throughout the fermentation period, ranging from day 0 to day 12, under optimized conditions. The results consistently demonstrated an initial increase in antioxidant activity from day 0 to 6, followed by a decline from day 6 to 12. Notably, statistical analysis revealed that the antioxidant activity of the test sample was significantly better (p > 0.001) compared to the control sample. The nutritional content of the kombucha from day 6 of the test sample is higher than the control sample provided sugars (fructose 0.4 ± 0.1, glucose 0.7 ± 0.1, sucrose 1.4 ± 0.1) g/100 mL, minerals (calcium, 19.4 ± 0.15, iron 23.1 ± 0.25, and potassium 28.3 ± 0.25) mg/100 mL, vitamins (B1 0.58 ± 0.01, B2 0.30 ± 0.02, B3 0.33 ± 0.02, B6 0.75 ± 0.02, B9 0.19 ± 0.03, B12 0.9 ± 0.03, and C 1.38 ± 0.06) mg/100 mL, sodium 4.35 ± 0.25 mg/100 mL, calories 14.85 ± 0.25 mg/100 mL, carbohydrates 3.135 ± 0.12, and acids (acetic acid 4.20 ± 0.02, glucuronic acid 1.78 ± 0.02) mg/100 mL on day 12. The predominant microbial species identified in both control and test samples included Komagataeibacter rhaeticus, Gluconobacter oxydans, Brettanomyces bruxellensis, and Zygosaccharomyces bailli, each with varying dominance levels. These microorganisms play essential roles in metabolizing sugars, generating acids, and contributing to the distinctive flavor profile of kombucha. Sensory evaluations of the control and test samples were analyzed, and the overall preference was 88% for the test sample with tea dust and molasses. The sensory characteristics of the test sample included a fruity smell (41%), fizzy texture (66%), bright color (47%), and a fruity taste (67%), with overall acceptability (56%) rating it as excellent. Our research contributes to a deeper understanding of the interplay between raw materials, microbial composition, and the resulting composition of bioactive compounds.

Optimizing enzyme properties to enhance dihydroxyacetone production via methylglyoxal biosensor development

BACKGROUND

Dihydroxyacetone (DHA) stands as a crucial chemical material extensively utilized in the cosmetics industry. DHA production through the dephosphorylation of dihydroxyacetone phosphate, an intermediate product of the glycolysis pathway in Escherichia coli, presents a prospective alternative for industrial production. However, insights into the pivotal enzyme, dihydroxyacetone phosphate dephosphorylase (HdpA), remain limited for informed engineering. Consequently, the development of an efficient tool for high-throughput screening of HdpA hypermutants becomes imperative.

RESULTS

This study introduces a methylglyoxal biosensor, based on the formaldehyde-responding regulator FrmR, for the selection of HdpA. Initial modifications involved the insertion of the FrmR binding site upstream of the -35 region and into the spacer region between the -10 and -35 regions of the constitutive promoter J23110. Although the hybrid promoter retained constitutive expression, expression of FrmR led to complete repression. The addition of 350 μM methylglyoxal promptly alleviated FrmR inhibition, enhancing promoter activity by more than 40-fold. The methylglyoxal biosensor system exhibited a gradual increase in fluorescence intensity with methylglyoxal concentrations ranging from 10 to 500 μM. Notably, the biosensor system responded to methylglyoxal spontaneously converted from added DHA, facilitating the separation of DHA producing and non-producing strains through flow cytometry sorting. Subsequently, the methylglyoxal biosensor was successfully applied to screen a library of HdpA mutants, identifying two strains harboring specific mutants 267G > T and D110G/G151C that showed improved DHA production by 68% and 114%, respectively. Expressing of these two HdpA mutants directly in a DHA-producing strain also increased DHA production from 1.45 to 1.92 and 2.29 g/L, respectively, demonstrating the enhanced enzyme properties of the HdpA mutants.

CONCLUSIONS

The methylglyoxal biosensor offers a novel strategy for constructing genetically encoded biosensors and serves as a robust platform for indirectly determining DHA levels by responding to methylglyoxal. This property enables efficiently screening of HdpA hypermutants to enhance DHA production.

Expression of a recombinant protein by an acetic acid bacterial host

We evaluated the suitability of Komagataeibacter europaeus, a vinegar production organism adept at synthetic media growth, as a host for heterologous gene expression. Cryptic plasmids (pGE1 and pGE2 derivatives) from K. europaeus strain KGMA0119 were employed as vectors for heterologous gene expression. The focus was placed on the groES promoter as a potential inducible switch. The groES promoter was fused with the EGFP gene and introduced into a pGE1 derivative to assess its suitability. Ethanol, acetic acid, and heat stresses were examined under various conditions for induction. EGFP transcription surged 600-fold when late logarithmic phase K. europaeus cells, cultured at 30 °C, endured heat stress at 40 °C, coupled with 20% acetic acid and 30% ethanol stress after an additional 6-hour cultivation. This robust induction system was then applied to express two proteins, Tth pol from the thermophilic bacterium Thermus thermophilus strain M1 and UPV230, a restriction enzyme from the acid-tolerant microorganism Ureaplasma parvum, known to cause vaginal infections and miscarriages. Both Tth pol and UPV230 were successfully expressed in K. europaeus cells and purified. The recovery of Tth pol from K. europaeus cells (480 µg protein per liter culture) was approximately half that from E. coli (960 µg protein per liter culture). In contrast, UPV230 recovery from K. europaeus cells (640 µg protein per liter culture) was nearly 10 times higher than that from Escherichia coli (66 µg protein per liter). The data highlights the potential of acetic acid bacteria as a host for producing acidophilic proteins. The shift in recognition from a 6-base sequence to a 4-base sequence of UPV230 was observed, accompanied by a change in structure as the pH transitioned from acidic pH to near-neutral pH.

Thermodynamics of microbial consortia: Enthalpies and Gibbs energies of microorganism live matter and macromolecules of E. coli, G. oxydans, P. fluorescens, S. thermophilus and P. chrysogenum

Every microorganism represents a biothermodynamic system, characterized by an empirical formula and thermodynamic properties of biosynthesis. Gibbs energy of biosynthesis influences the multiplication rate of a microorganism. In case of a mixed culture (microbial consortia) biosynthesis processes of microbial species are competitive. This is why Gibbs energy of biosynthesis determines the growth in a mixed culture. This paper gives a mechanistic model that explains growth of microorganisms in mixed culture and ability to grow in microbial consortia. Detailed biosynthesis reactions were formulated for the first time for five microorganism species, which include metallic elements. Moreover, thermodynamic properties of live matter and biosynthesis were calculated for the first time for five microorganism species and macromolecules.

Interfacing Whole Cell Biocatalysis with a Biocompatible Pictet-Spengler Reaction for One-Pot Syntheses of Tetrahydroisoquinolines and Tryptolines

Biocatalytic processes are highly selective and specific. However, their utility is limited by the comparatively narrow scope of enzyme-catalysed transformations. To expand product scope, we are developing biocompatible processes that combine biocatalytic reactions with chemo-catalysis in single-flask processes. Here, we show that a chemocatalysed Pictet-Spengler annulation can be interfaced with biocatalysed alcohol oxidation. This two-step, one-pot cascade reaction converts tyramine and aliphatic alcohols to tetrahydroisoquinoline alkaloids in aqueous buffer at mild pH. Tryptamine derivatives are also efficiently converted to tryptolines. Optimization of stoichiometry, pH, reaction time, and whole-cell catalyst deliver the tetrahydroisouinolines and tryptolines in >90 % and >40 % isolated yield, respectively, with excellent regioselectivity.

Efficient production of 2-keto-L-gulonic acid from D-glucose in Gluconobacter oxydans ATCC9937 by mining key enzyme and transporter

Direct production of 2-keto-L-gulonic acid (2-KLG, the precursor of vitamin C) from D-glucose through 2,5-diketo-D-gluconic acid (2,5-DKG) is a promising alternative route. To explore the pathway of producing 2-KLG from D-glucose, Gluconobacter oxydans ATCC9937 was selected as a chassis strain. It was found that the chassis strain naturally has the ability to synthesize 2-KLG from D-glucose, and a new 2,5-DKG reductase (DKGR) was found on its genome. Several major issues limiting production were identified, including the insufficient catalytic capacity of DKGR, poor transmembrane movement of 2,5-DKG and imbalanced D-glucose consumption flux inside and outside of the host strain cells. By identifying novel DKGR and 2,5-DKG transporter, the whole 2-KLG biosynthesis pathway was systematically enhanced by balancing intracellular and extracellular D-glucose metabolic flux. The engineered strain produced 30.5 g/L 2-KLG with a conversion ratio of 39.0%. The results pave the way for a more economical large-scale fermentation process for vitamin C.

New perspectives into Gluconobacter-catalysed biotransformations

Different from other aerobic microorganisms that oxidise carbon sources to water and carbon dioxide, Gluconobacter catalyses the incomplete oxidation of various substrates with regio- and stereoselectivity. This ability, as well as its capacity to release the resulting products into the reaction media, place Gluconobacter as a privileged member of a non-model microorganism class that may boost industrial biotechnology. Knowledge of new technologies applied to Gluconobacter has been piling up in recent years. Advancements in its genetic modification, application of immobilisation tools and careful designs of the transformations, have improved productivities and stabilities of Gluconobacter strains or enabled new bioconversions for the production of valuable marketable chemicals. In this work, the latest advancements applied to Gluconobacter-catalysed biotransformations are summarised with a special focus on recent available tools to improve them. From genetic and metabolic engineering to bioreactor design, the most recent works on the topic are analysed in depth to provide a comprehensive resource not only for scientists and technologists working on/with Gluconobacter, but for the general biotechnologist.

Low pH Stress Enhances Gluconic Acid Accumulation with Enzymatic Hydrolysate as Feedstock Using Gluconobacter oxydans

Gluconic acid has been increasingly in demand in recent years due to the wide applications in the food, healthcare and construction industries. Plant-derived biomass is rich in biopolymers that comprise glucose as the monomeric unit, which provide abundant feedstock for gluconic acid production. Gluconobacter oxydans can rapidly and incompletely oxidize glucose to gluconic acid and it is regarded as ideal industrial microorganism. Once glucose is depleted, the gluconic acid will be further bio-oxidized to 2-ketogluconic acid by Gluconobacter oxydans. The endpoint is difficult to be controlled, especially in an industrial fermentation process. In this study, it was found that the low pH environment (2.5~3.5) could limit the further metabolism of gluconic acid and that it resulted in a yield over 95%. Therefore, the low pH stress strategy for efficiently producing gluconic acid from biomass-derived glucose was put forward and investigated with enzymatic hydrolysate. As a result, 98.8 g/L gluconic acid with a yield of 96% could be obtained from concentrated corncob enzymatic hydrolysate that initially contained 100 g/L glucose with 1.4 g/L cells loading of Gluconobacter oxydans. In addition, the low pH stress strategy could effectively control end-point and decrease the risk of microbial contamination. Overall, this strategy provides a potential for industrial gluconic acid production from lignocellulosic materials.

Polymer-Based Conductive Nanocomposites for the Development of Bioanodes Using Membrane-Bound Enzyme Systems of Bacteria Gluconobacter oxydans in Biofuel Cells

The development of biofuel cells (BFCs) currently has high potential since these devices can be used as alternative energy sources. This work studies promising materials for biomaterial immobilization in bioelectrochemical devices based on a comparative analysis of the energy characteristics (generated potential, internal resistance, power) of biofuel cells. Bioanodes are formed by the immobilization of membrane-bound enzyme systems of Gluconobacter oxydans VKM V-1280 bacteria containing pyrroloquinolinquinone-dependent dehydrogenases into hydrogels of polymer-based composites with carbon nanotubes. Natural and synthetic polymers are used as matrices, and multi-walled carbon nanotubes oxidized in hydrogen peroxide vapor (MWCNTox) are used as fillers. The intensity ratio of two characteristic peaks associated with the presence of atoms C in the sp³ and sp² hybridization for the pristine and oxidized materials is 0.933 and 0.766, respectively. This proves a reduced degree of MWCNTox defectiveness compared to the pristine nanotubes. MWCNTox in the bioanode composites significantly improve the energy characteristics of the BFCs. Chitosan hydrogel in composition with MWCNTox is the most promising material for biocatalyst immobilization for the development of bioelectrochemical systems. The maximum power density was 1.39 × 10^-5 W/mm², which is 2 times higher than the power of BFCs based on other polymer nanocomposites.

Exploring the Core Microbiota of Four Different Traditional Fermented Beverages from the Colombian Andes

Fermentation is an ancient process used to prepare and preserve food. Currently, fermented beverages are part of the culture of people living in the Colombian Andean Region, and they are a vital part of their cosmology and ancestral vision. Chicha, Forcha, Champús, and Masato are some of the most common Colombian Andes region’s traditional fermented beverages. These drinks come from the fermentation of maize (Zea maize), but other cereals such as wheat or rye, could be used. The fermentation is carried out by a set of bacteria and yeasts that provide characteristic organoleptic properties of each beverage. In this work, the information collected from the metagenomics analyses by sequencing ITS 1-4 (Internal Transcriber Spacer) and the 16S ribosomal gene for fungi and the V3-V4 region of the rDNA for bacteria allowed us to identify the diversity present in these autochthonous fermented beverages made with maize. The sequencing analysis showed the presence of 39 bacterial and 20 fungal genera. In addition, we determined that only nine genera of bacteria and two genera of fungi affect the organoleptic properties of smell, colour, and flavour, given the production of compounds such as lactic acid, alcohol, and phenols, highlighting the critical role of these microorganisms. Our findings provide new insights into the core microbiota of these beverages, represented by Lactobacillus fermentum, Acetobacter pasteurianus, and Saccharomyces cerevisiae.

Efficient 1,3-dihydroxyacetone biosynthesis in Gluconobacter oxydans using metabolic engineering and a fed-batch strategy

1,3-Dihydroxyacetone (DHA) is a commercially important chemical and widely used in cosmetics, pharmaceuticals, and food industries as it prevents excessive water evaporation, and provides anti-ultraviolet radiation protection and antioxidant activity. Currently, the industrial production of DHA is based on a biotechnological synthetic route using Gluconobacter oxydans. However, achieving higher production requires more improvements in the synthetic process. In this study, we compared DHA synthesis levels in five industrial wild-type Gluconobacter strains, after which the G. oxydans WSH-003 strain was selected. Then, 16 dehydrogenase genes, unrelated to DHA synthesis, were individually knocked out, with one strain significantly enhancing DHA production, reaching 89.49 g L-1 and 42.27% higher than the wild-type strain. By optimizing the culture media, including seed culture and fermentation media, DHA production was further enhanced. Finally, using an established fed-batch fermentation system, DHA production reached 198.81 g L-1 in a 5 L bioreactor, with a glycerol conversion rate of 82.84%.

Characterization of Physicochemical Properties of Melanin Produced by Gluconobacter oxydans FBFS 97

The present study aimed to characterize melanin pigment extracted from Gluconobacter oxydans FBFS 97. After 14 days of culture at 28 °C in GY (glucose and yeast extract) liquid-state medium, G. oxydans FBFS97 produce the maximum melanin, up to about 12–15 mg/L. The physicochemical characteristics of the extracted melanin showed an ability to dissolve in 1 mol/L NaOH or 1 mol/L KOH, and insolubility in water and most organic solvents, such as chloroform and petroleum ether. The extracted melanin was confirmed to be exact melanin by ultraviolet-visible spectrophotometry, Fourier-transform infrared spectroscopy, thin-layer chromatography, elemental analysis, and scanning electron microscopy. The UV-visible spectrum of G. oxydans FBFS97 exhibited a maximum absorption peak at 230 nm. Extracted melanin demonstrated significant free radical-scavenging activity by DPPH and ABTS methods. The IC50 value of the extracted melanin for scavenging 50% DPPH radicals was 36.94 μg/mL, and the IC50 value of antioxidant activity for ABTS was 4.06 μg/mL. Hence, G. oxydans FBFS97 has the potential to be a new candidate for melanin production.

The l-rhamnose-dependent regulator RhaS and its target promoters from Escherichia coli expand the genetic toolkit for regulatable gene expression in the acetic acid bacterium Gluconobacter oxydans

For regulatable target gene expression in the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first plasmids became available. These systems solely enable AraC- and TetR-dependent induction. In this study we showed that the l-rhamnose-dependent regulator RhaS from Escherichia coli and its target promoters P_rhaBAD, P_rhaT, and P_rhaSR could also be used in G. oxydans for regulatable target gene expression. Interestingly, in contrast to the responsiveness in E. coli, in G. oxydans RhaS increased the expression from P_rhaBAD in the absence of l-rhamnose and repressed P_rhaBAD in the presence of l-rhamnose. Inserting an additional RhaS binding site directly downstream from the −10 region generating promoter variant P_{rhaBAD(+RhaS-BS)} almost doubled the apparent RhaS-dependent promoter strength. Plasmid-based P_rhaBAD and P_{rhaBAD(+RhaS-BS)} activity could be reduced up to 90% by RhaS and l-rhamnose, while a genomic copy of P_{rhaBAD(+RhaS-BS)} appeared fully repressed. The RhaS-dependent repression was largely tunable by l-rhamnose concentrations between 0% and only 0.3% (w/v). The RhaS-P_rhaBAD and the RhaS-P_{rhaBAD(+RhaS-BS)} systems represent the first heterologous repressible expression systems for G. oxydans. In contrast to P_rhaBAD, the E. coli promoter P_rhaT was almost inactive in the absence of RhaS. In the presence of RhaS, the P_rhaT activity in the absence of l-rhamnose was weak, but could be induced up to 10-fold by addition of l-rhamnose, resulting in a moderate expression level. Therefore, the RhaS-P_rhaT system could be suitable for tunable low-level expression of difficult enzymes or membrane proteins in G. oxydans. The insertion of an additional RhaS binding site directly downstream from the E. coli P_rhaT −10 region increased the non-induced expression strength and reversed the regulation by RhaS and l-rhamnose from inducible to repressible. The P_rhaSR promoter appeared to be positively auto-regulated by RhaS and this activation was increased by l-rhamnose. In summary, the interplay of the l-rhamnose-binding RhaS transcriptional regulator from E. coli with its target promoters P_rhaBAD, P_rhaT, P_rhaSR and variants thereof provide new opportunities for regulatable gene expression in G. oxydans and possibly also for simultaneous l-rhamnose-triggered repression and activation of target genes, which is a highly interesting possibility in metabolic engineering approaches requiring redirection of carbon fluxes.