Genetic analysis of D-xylose metabolism pathways in Gluconobacter oxydans 621H

Screening of Gluconobacter oxydans in xylonic acid fermentation for tolerance of the inhibitors formed dilute acid pretreatment

Pre-hydrolysate liquor, as an inevitable by-product, contains a large amount of xylose, and is therefore an inexpensive feedstock that can be upgraded to value-added chemical xylonic acid. However, inhibitors, simultaneously formed in lignocellulose pretreatment process, are regarded as the major obstacle for effectively bio-converting xylose in pre-hydrolysate into xylonic acid. In this study, Gluconobacter oxydans, with highly selective and efficient, was employed for xylonic acid production; the impacts of five typical toxic inhibitory compounds on xylonic acid productivity and the activity of the membrane-bound dehydrogenase were evaluated. The results revealed that the inhibitors showed different degrees of influence toward xylonic acid production, and the order of inhibitory effect for acidic inhibitors was formic acid > acetic acid > levulinic acid; the inhibitory effect of aldehyde inhibitors was furfural > 5-hydroxymethyl-furfural. This study provides an important basis of metabolic modification and detoxification process for enhancing inhibitor tolerance and xylonic acid productivity.

Overexpression of mGDH in Gluconobacter oxydans to improve D-xylonic acid production from corn stover hydrolysate

Background

d-Xylonic acid is a versatile platform chemical with broad potential applications as a water reducer and disperser for cement and as a precursor for 1,4-butanediol and 1,2,4-tributantriol. Microbial production of d-xylonic acid with bacteria such as Gluconobacter oxydans from inexpensive lignocellulosic feedstock is generally regarded as one of the most promising and cost-effective methods for industrial production. However, high substrate concentrations and hydrolysate inhibitors reduce xylonic acid productivity.

Results

The d-xylonic acid productivity of G. oxydans DSM2003 was improved by overexpressing the mGDH gene, which encodes membrane-bound glucose dehydrogenase. Using the mutated plasmids based on pBBR1MCS-5 in our previous work, the recombinant strain G. oxydans/pBBR-R3510-mGDH was obtained with a significant improvement in d-xylonic acid production and a strengthened tolerance to hydrolysate inhibitors. The fed-batch biotransformation of d-xylose by this recombinant strain reached a high titer (588.7 g/L), yield (99.4%), and volumetric productivity (8.66 g/L/h). Moreover, up to 246.4 g/L d-xylonic acid was produced directly from corn stover hydrolysate without detoxification at a yield of 98.9% and volumetric productivity of 11.2 g/L/h. In addition, G. oxydans/pBBR-R3510-mGDH exhibited a strong tolerance to typical inhibitors, i.e., formic acid, furfural, and 5-hydroxymethylfurfural.

Conclusion

Through overexpressing mgdh in G. oxydans, we obtained the recombinant strain G. oxydans/pBBR-R3510-mGDH, and it was capable of efficiently producing xylonic acid from corn stover hydrolysate under high inhibitor concentrations. The high d-xylonic acid productivity of G. oxydans/pBBR-R3510-mGDH made it an attractive choice for biotechnological production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01763-y.

Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism

Herbaspirillum seropedicae is a β-proteobacterium that establishes as an endophyte in various plants. These bacteria can consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolic pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature and some microorganisms, including H. seropedicae, are able to accumulate poly-3-hydroxybutyrate when consuming this pentose as a carbon source. In this work, we present a study of D-xylose catabolic pathways in H. seropedicae strain Z69 using RNA-seq analysis and subsequent analysis of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD⁺-dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This appears to be due to the expression of an L-arabinose dehydrogenase, encoded by the araB gene (G5B88_05250), that can use D-xylose as a substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: the Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that synthesizes pyruvate and glycolate. This novel pathway appears to contribute to D-xylose metabolism, since a mutant in the last step, Z69∆mhpD, was able to grow on this pentose only after an extended lag phase (40-50 h). KEY POINTS: • xylB gene (G5B88_22805) encodes a NAD⁺-dependent D-xylose dehydrogenase. • araB gene (G5B88_05250) encodes a L-arabinose dehydrogenase able to recognize D-xylose. • A novel route involving mhpD gene is preferred for D-xylose catabolism.

Adaptive evolution of Gluconobacter oxydans accelerates the conversion rate of non-glucose sugars derived from lignocellulose biomass

Gluconobacter oxydans is capable of oxidizing various lignocellulose derived sugars into the corresponding sugar acids including glucose, xylose, arabinose, galactose and mannose, but simultaneous utilization of these sugars is difficult. This study attempted an adaptive evolution of G. oxydans by alternate transfer in inhibitors containing hydrolysate and inhibitors free hydrolysate for intensifying sugars simultaneous utilization. After 420 days' continuous culture, the conversion rate of all non-glucose sugars significantly improved by several folds and achieved complete conversion of lignocellulose-derived sugars to the corresponding sugar acids. The significant up-regulation of mGDH gene in the adapted G. oxydans strain (more than 40-fold greater than the parental) was considered as the decisive factor for the improvement of strain performance. This evolution adaptation strategy also could be used to accelerate robust sugars utilization for other fermented strains in lignocellulose biorefinery.

Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way

Background

Whole cells of Gluconobacter oxydans are widely used in various biocatalytic processes. Sorbitol at high concentrations is commonly used in complex media to prepare biocatalysts. Exploiting an alternative process for preparation of biocatalysts with low cost substrates is of importance for industrial applications.

Results

G. oxydans 621H was confirmed to have the ability to grow in mineral salts medium with glycerol, an inevitable waste generated from industry of biofuels, as the sole carbon source. Based on the glycerol utilization mechanism elucidated in this study, the major polyol dehydrogenase (GOX0854) and the membrane-bound alcohol dehydrogenase (GOX1068) can competitively utilize glycerol but play no obvious roles in the biocatalyst preparation. Thus, the genes related to these two enzymes were deleted. Whole cells of G. oxydans ∆GOX1068∆GOX0854 can be prepared from glycerol with a 2.4-fold higher biomass yield than that of G. oxydans 621H. Using whole cells of G. oxydans ∆GOX1068∆GOX0854 as the biocatalyst, 61.6 g L⁻¹ xylonate was produced from 58.4 g L⁻¹ xylose at a yield of 1.05 g g⁻¹.

Conclusion

This process is an example of efficient preparation of whole cells of G. oxydans with reduced cost. Besides xylonate production from xylose, other biocatalytic processes might also be developed using whole cells of metabolic engineered G. oxydans prepared from glycerol.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1001-0) contains supplementary material, which is available to authorized users.

Process for calcium xylonate production as a concrete admixture derived from in-situ fermentation of wheat straw pre-hydrolysate

One of the major obstacles in process of lignocellulosic biorefinery is the utilization of pre-hydrolysate from pre-treatment. Although lignocellulosic pre-hydrolysate can serve as an economic starting material for xylonic acid production, the advancement of xylonic acid or xylonate is still limited by further commercial value or applications. In the present study, xylose in the high concentration wheat straw pre-hydrolysate was first in-situ biooxidized to xylonate by Gluconobacter oxydans. To meet the needs of commercialization, crude powdered calcium xylonate was prepared by drying process and calcium xylonate content in the prepared crude product was more than 70%. Then, the calcium xylonate product was evaluated as concrete admixture without any complex purification steps and the results demonstrated that xylonate could improve the performance of concrete. Overall, the crude xylonate product directly produced from low-cost wheat straw pre-hydrolysate can potentially be developed as retarding reducer, which could subsequently benefit lignocellulosic biorefinery.

Genome-centric view of carbon processing in thawing permafrost

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms

The D-xylose oxidative pathway (XOP) has recently been employed in several recombinant microorganisms for growth or for the production of several valuable compounds. The XOP is initiated by D-xylose oxidation to D-xylonolactone, which is then hydrolyzed into D-xylonic acid. D-Xylonic acid is then dehydrated to form 2-keto-3-deoxy-D-xylonic acid, which may be further dehydrated then oxidized into α-ketoglutarate or undergo aldol cleavage to form pyruvate and glycolaldehyde. This review introduces a brief discussion about XOP and its discovery in bacteria and archaea, such as Caulobacter crescentus and Haloferax volcanii. Furthermore, the current advances in the metabolic engineering of recombinant strains employing the XOP are discussed. This includes utilization of XOP for the production of diols, triols, and short-chain organic acids in Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum. Improving the D-xylose uptake, growth yields, and product titer through several metabolic engineering techniques bring some of these recombinant strains close to industrial viability. However, more developments are still needed to optimize the XOP pathway in the host strains, particularly in the minimization of by-product formation.

Simultaneous Bioconversion of Xylose and Glycerol to Xylonic Acid and 1,3-Dihydroxyacetone from the Mixture of Pre-Hydrolysates and Ethanol-Fermented Waste Liquid by Gluconobacter oxydans

Simultaneous bioconversion of xylose and glycerol to xylonic acid and 1,3-dihydroxyacetone (DHA) was realized by using Gluconobacter oxydans (G. oxydans). Currently, the enzymatic hydrolysate to ethanol-fermented waste liquid and the inorganic acid pre-hydrolysate that contain abundant glycerol and xylose were difficult to be utilized or disposed. Based on the method of compressed oxygen supply-sealed and stirred tank reactor system (COS-SSTR), the xylonic acid and 1,3-dihydroxyacetone could be co-produced rapidly with the mixture of the dilute sulfuric acid pre-hydrolysate and ethanol-fermented waste liquid of enzymatic hydrolysate (MPEW) as material. By means of the system, we finally produced 102.3 ± 3.2 g/L xylonic acid and 40.6 ± 1.8 g/L 1,3-dihydroxyacetone at yield of 92.4 ± 2.8 % and 80.6 ± 3.5 % directly and simultaneously from the mixed solution. The central features of this bioprocess application would enable cost-competitive bacterial xylonic acid and 1,3-dihydroxyacetone production from lignocellulosic materials.