Kinetic study on succinic acid and acetic acid formation during continuous cultures of Anaerobiospirillum succiniciproducens grown on glycerol

Genetic optimization of the human gut bacterium Phocaeicola vulgatus for enhanced succinate production

The demand for sustainably produced bulk chemicals is constantly rising. Succinate serves as a fundamental component in various food, chemical, and pharmaceutical products. Succinate can be produced from sustainable raw materials using microbial fermentation and enzyme-based technologies. Bacteroides and Phocaeicola species, widely distributed and prevalent gut commensals, possess enzyme sets for the metabolization of complex plant polysaccharides and synthesize succinate as a fermentative end product. This study employed novel molecular techniques to enhance succinate yields in the natural succinate producer Phocaeicola vulgatus by directing the metabolic carbon flow toward succinate formation. The deletion of the gene encoding the methylmalonyl-CoA mutase (Δmcm, bvu_0309-0310) resulted in a 95% increase in succinate production, as metabolization to propionate was effectively blocked. Furthermore, deletion of genes encoding the lactate dehydrogenase (Δldh, bvu_2499) and the pyruvate:formate lyase (Δpfl, bvu_2880) eliminated the formation of fermentative end products lactate and formate. By overproducing the transketolase (TKT, BVU_2318) in the triple deletion mutant, succinate production increased from 3.9 mmol/g dry weight in the wild type to 10.9 mmol/g dry weight. Overall, succinate yield increased by 180% in the new mutant strain P. vulgatus Δmcm Δldh Δpfl pG106_tkt relative to the parent strain. This approach is a proof of concept, verifying the genetic accessibility of P. vulgatus, and forms the basis for targeted genetic optimization. The increase of efficiency highlights the huge potential of P. vulgatus as a succinate producer with applications in sustainable bioproduction processes. KEY POINTS: • Deleting methylmalonyl-CoA mutase gene in P. vulgatus doubled succinate production • Triple deletion mutant with transketolase overexpression increased succinate yield by 180% • P. vulgatus shows high potential for sustainable bulk chemical production via genetic optimization.

Substrate type and CO2 addition significantly influence succinic acid production of Basfia succiniciproducens

Metabolic engineering has shown that optimizing metabolic pathways' fluxes for industrial purposes requires a methodical approach. Accordingly, in this study, in silico metabolic modeling was utilized to characterize the lesser-known strain Basfia succiniciproducens under different environmental conditions, followed by the use of industrially relevant substrates for succinic acid synthesis. Based on RT-qPCR carried out in flask experiments, we discovered a relatively large difference in the expression levels of ldhA gene compared to glucose in both xylose and glycerol cultures. In bioreactor-scale fermentations, the impact of different gas phases (CO2, CO2/AIR) on biomass yield, substrate consumption, and metabolite profiles was also investigated. In the case of glycerol, the addition of CO2 increased biomass as well as target product formation, while using CO2/AIR gas phase resulted in higher target product yield (0.184 mM⋅mM-1). In case of xylose, using CO2 alone would result in higher succinic acid production (0.277 mM⋅mM-1). The promising rumen bacteria, B. succiniciproducens, has shown to be suitable for succinic acid production from both xylose and glycerol. As a result, our findings present new opportunities for broadening the range of raw materials used in this significant biochemical process. Our study also sheds light on fermentation parameter optimization for this strain, namely that, CO2/AIR supply has a positive effect on target product formation.

Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli

INTRODUCTION

Glycerol is a byproduct from the biodiesel industry that can be biotransformed by Escherichia coli to high added-value products such as succinate under aerobic conditions. The main genetic engineering strategies to achieve this aim involve the mutation of succinate dehydrogenase (sdhA) gene and also those responsible for acetate synthesis including acetate kinase, phosphate acetyl transferase and pyruvate oxidase encoded by ackA, pta and pox genes respectively in the ΔsdhAΔack-ptaΔpox (M4) mutant. Other genetic manipulations to rewire the metabolism toward succinate consist on the activation of the glyoxylate shunt or blockage the pentose phosphate pathway (PPP) by deletion of isocitrate lyase repressor (iclR) or gluconate dehydrogenase (gnd) genes on M4-ΔiclR and M4-Δgnd mutants respectively.

OBJECTIVE

To deeply understand the effect of the blocking of the pentose phosphate pathway (PPP) or the activation of the glyoxylate shunt, metabolite profiles were analyzed on M4-Δgnd, M4-ΔiclR and M4 mutants.

METHODS

Metabolomics was performed by FT-IR and GC-MS for metabolite fingerprinting and HPLC for quantification of succinate and glycerol.

RESULTS

Most of the 65 identified metabolites showed lower relative levels in the M4-ΔiclR and M4-Δgnd mutants than those of the M4. However, fructose 1,6-biphosphate, trehalose, isovaleric acid and mannitol relative concentrations were increased in M4-ΔiclR and M4-Δgnd mutants. To further improve succinate production, the synthesis of mannitol was suppressed by deletion of mannitol dehydrogenase (mtlD) on M4-ΔgndΔmtlD mutant that increase ~ 20% respect to M4-Δgnd.

CONCLUSION

Metabolomics can serve as a holistic tool to identify bottlenecks in metabolic pathways by a non-rational design. Genetic manipulation to release these restrictions could increase the production of succinate.

Biochemical biorefinery: A low-cost and non-waste concept for promoting sustainable circular bioeconomy

The transition from a fossil-based linear economy to a circular bioeconomy is no longer an option but rather imperative, given worldwide concerns about the depletion of fossil resources and the demand for innovative products that are ecocompatible. As a critical component of sustainable development, this discourse has attracted wide attention at the regional and international levels. Biorefinery is an indispensable technology to implement the blueprint of the circular bioeconomy. As a low-cost, non-waste innovative concept, the biorefinery concept will spur a myriad of new economic opportunities across a wide range of sectors. Consequently, scaling up biorefinery processes is of the essence. Despite several decades of research and development channeled into upscaling biorefinery processes, the commercialization of biorefinery technology appears unrealizable. In this review, challenges limiting the commercialization of biorefinery technologies are discussed, with a particular focus on biofuels, biochemicals, and biomaterials. To counteract these challenges, various process intensification strategies such as consolidated bioprocessing, integrated biorefinery configurations, the use of highly efficient bioreactors, simultaneous saccharification and fermentation, have been explored. This study also includes an overview of biomass pretreatment-generated inhibitory compounds as platform chemicals to produce other essential biocommodities. There is a detailed examination of the technological, economic, and environmental considerations of a sustainable biorefinery. Finally, the prospects for establishing a viable circular bioeconomy in Nigeria are briefly discussed.

Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability

Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO₂ and CH₄) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.

Valorization of Biodiesel Byproduct Crude Glycerol for the Production of Bioenergy and Biochemicals

The rapid growth of global biodiesel production requires simultaneous effective utilization of glycerol obtained as a by-product of the transesterification process. Accumulation of the byproduct glycerol from biodiesel industries can lead to considerable environment issues. Hence, there is extensive research focus on the transformation of crude glycerol into value-added products. This paper makes an overview of the nature of crude glycerol and ongoing research on its conversion to value-added products. Both chemical and biological routes of glycerol valorization will be presented. Details of crude glycerol conversion into microbial lipid and subsequent products will also be highlighted.

Technologies for Biogas Upgrading to Biomethane: A Review

The environmental impacts and high long-term costs of poor waste disposal have pushed the industry to realize the potential of turning this problem into an economic and sustainable initiative. Anaerobic digestion and the production of biogas can provide an efficient means of meeting several objectives concerning energy, environmental, and waste management policy. Biogas contains methane (60%) and carbon dioxide (40%) as its principal constituent. Excluding methane, other gasses contained in biogas are considered as contaminants. Removal of these impurities, especially carbon dioxide, will increase the biogas quality for further use. Integrating biological processes into the bio-refinery that effectively consume carbon dioxide will become increasingly important. Such process integration could significantly improve the sustainability of the overall bio-refinery process. The biogas upgrading by utilization of carbon dioxide rather than removal of it is a suitable strategy in this direction. The present work is a critical review that summarizes state-of-the-art technologies for biogas upgrading with particular attention to the emerging biological methanation processes. It also discusses the future perspectives for overcoming the challenges associated with upgradation. While biogas offers a good substitution for fossil fuels, it still not a perfect solution for global greenhouse gas emissions and further research still needs to be conducted.

Recent advances in the production of value added chemicals and lipids utilizing biodiesel industry generated crude glycerol as a substrate - Metabolic aspects, challenges and possibilities: An overview

One of the major ecological concerns associated with biodiesel production is the generation of waste/crude glycerol during the trans-esterification process. Purification of this crude glycerol is not economically viable. In this context, the development of an efficient and economically viable strategy would be biotransformation reactions converting the biodiesel derived crude glycerol into value added chemicals. Hence the process ensures the sustainability and waste management in biodiesel industry, paving a path to integrated biorefineries. This review addresses a waste to wealth approach for utilization of crude glycerol in the production of value added chemicals, current trends, challenges, future perspectives, metabolic approaches and the genetic tools developed for the improved synthesis over wild type microorganisms were described.

Continuous succinic acid production from xylose by Actinobacillus succinogenes

Continuous, anaerobic fermentations of D-xylose were performed by Actinobacillus succinogenes 130Z in a custom, biofilm reactor at dilution rates of 0.05, 0.10 and 0.30 h(-1). Succinic acid yields on xylose (0.55-0.68 g g(-1)), titres (10.9-29.4 g L(-1)) and productivities (1.5-3.4 g L(-1) h(-1)) were lower than those of a previous study on glucose, but product ratios (succinic acid/acetic acid = 3.0-5.0 g g(-1)) and carbohydrate consumption rates were similar. Also, mass balance closures on xylose were up to 18.2 % lower than those on glucose. A modified HPLC method revealed pyruvic acid excretion at appreciable concentrations (1.2-1.9 g L(-1)) which improved the mass balance closure by up to 16.8 %. Furthermore, redox balances based on the accounted xylose consumed and the excreted metabolites, indicated an overproduction of reducing power. The oxidative pentose phosphate pathway was shown to be a plausible source of the additional reducing power.

Conversion of agroindustrial residues for high poly(γ-glutamic acid) production by Bacillus subtilis NX-2 via solid-state fermentation

Poly(γ-glutamic acid) (γ-PGA) production by Bacillus subtilis NX-2 was carried out through solid-state fermentation with dry mushroom residues (DMR) and monosodium glutamate production residues (MGPR; a substitute of glutamate) for the first time. Dry shiitake mushroom residue (DSMR) was found to be the most suitable solid substrate among these DMRs; the optimal DSMR-to-MGPR ratio was optimized as 12:8. To increase γ-PGA production, industrial waste glycerol was added as a carbon source supplement to the solid-state medium. As a result, γ-PGA production increased by 34.8%. The batch fermentation obtained an outcome of 115.6 g kg(-1) γ-PGA and 39.5×10(8) colony forming units g(-1) cells. Furthermore, a satisfactory yield of 107.7 g kg(-1) γ-PGA was achieved by compost experiment on a scale of 50 kg in open air, indicating that economically large-scale γ-PGA production was feasible. Therefore, this study provided a novel method to produce γ-PGA from abundant and low-cost agroindustrial residues.

Respiratory glycerol metabolism of Actinobacillus succinogenes 130Z for succinate production

Actinobacillus succinogenes 130Z naturally produces among the highest levels of succinate from a variety of inexpensive carbon substrates. A few studies have demonstrated that A. succinogenes can anaerobically metabolize glycerol, a waste product of biodiesel manufacture and an inexpensive feedstock, to produce high yields of succinate. However, all these studies were performed in the presence of yeast extract, which largely removes the redox constraints associated with fermenting glycerol, a highly reduced molecule. We demonstrated that A. succinogenes cannot ferment glycerol in minimal medium, but that it can metabolize glycerol by aerobic or anaerobic respiration. These results were expected based on the A. succinogenes genome, which encodes respiratory enzymes, but no pathway for 1,3-propanediol production. We investigated A. succinogenes’s glycerol metabolism in minimal medium in a variety of respiratory conditions by comparing growth, metabolite production, and in vitro activity of terminal oxidoreductases. Nitrate inhibited succinate production by inhibiting fumarate reductase expression. In contrast, growth in the presence of dimethylsulfoxide and in microaerobic conditions allowed high succinate yields. The highest succinate yield was 0.75 mol/mol glycerol (75 % of the maximum theoretical yield) in continuous microaerobic cultures. A. succinogenes could also grow and produce succinate on partially refined glycerols obtained directly from biodiesel manufacture. Finally, by expressing a heterologous 1,3-propanediol synthesis pathway in A. succinogenes, we provide the first proof of concept that A. succinogenes can be engineered to grow fermentatively on glycerol.

Fermentative succinate production: an emerging technology to replace the traditional petrochemical processes

Succinate is a valuable platform chemical for multiple applications. Confronted with the exhaustion of fossil energy resources, fermentative succinate production from renewable biomass to replace the traditional petrochemical process is receiving an increasing amount of attention. During the past few years, the succinate-producing process using microbial fermentation has been made commercially available by the joint efforts of researchers in different fields. In this review, recent attempts and experiences devoted to reduce the production cost of biobased succinate are summarized, including strain improvement, fermentation engineering, and downstream processing. The key limitations and challenges faced in current microbial production systems are also proposed.

Directed pathway evolution of the glyoxylate shunt in Escherichia coli for improved aerobic succinate production from glycerol

α-Ketoglutarate is accumulated as the main byproduct during the aerobic succinate production from glycerol by Escherichia coli BL21(DE3) in minimal medium. To address this issue, here a strategy of directed pathway evolution was developed to enhance the alternative succinate production route-the glyoxylate shunt. Via the directed pathway evolution, the glyoxylate shunt was recruited as the primary anaplerotic pathway in a ppc mutant, which restored its viability in glycerol minimal medium. Subsequently, the operon sdhCDAB was deleted and the gene ppc was reverted in the evolved strain for succinate production. The resulting strain E2-Δsdh-ppc produced 30 % more succinate and 46 % less α-ketoglutarate than the control strain. A G583T mutation in gene icdA, which significantly decreased the activity of isocitrate dehydrogenase, was identified in the evolved strain as the main mutation responsible for the observed phenotype. Overexpression of α-ketoglutarate dehydrogenase complex in E2-Δsdh-ppc further reduced the amount of byproduct and improved succinate production. The final strain E2-Δsdh-ppc-sucAB produced 366 mM succinate from 1.3 M glycerol in minimal medium in fed-batch fermentation. The maximum and average succinate volumetric productivities were 19.2 and 6.55 mM h(-1), respectively, exhibiting potential industrial production capacity from the low-priced substrate.

Evolution of pyruvate kinase-deficient Escherichia coli mutants enables glycerol-based cell growth and succinate production

AIMS

The aim of this study was to engineer Escherichia coli strains that efficiently produce succinate from glycerol under anaerobic conditions after an aerobic growth phase.

METHODS AND RESULTS

We constructed E. coli strain ss195 with deletions of pykA and pykF, which resulted in slow growth on glycerol as sole carbon source. This growth defect was overcome by the selection of fast-growing mutants. Whole-genome resequencing of the evolved mutant ss251 identified the mutation A595S in PEP carboxylase (Ppc). Reverse metabolic engineering by introducing the wild-type allele revealed that this mutation is crucial for the described phenotype. Strain ss251 and derivatives thereof produced succinate with high yields above 80% mol mol(-1) from glycerol under nongrowth conditions.

CONCLUSIONS

The results show that during the aerobic growth of ss251, the formation of pyruvate proceeds via the proposed POMP pathway, starting with the carboxylation of PEP by Ppc. The resulting oxaloacetate is reduced by malate dehydrogenase (Mdh) to malate, which is then decarboxylated back to pyruvate by a malic enzyme (MaeA or MaeB). Mutation of ppc is crucial for fast growth of pykAF mutants on glycerol.

SIGNIFICANCE AND IMPACT OF STUDY

An E. coli mutant that is capable of achieving high yields of succinate (a top valued-added chemical) from glycerol (an abundant carbon source) was constructed. The identified ppc mutation could be applied to other production strains that require strong PEP carboxylation fluxes.

Succinate production in Escherichia coli

Succinate has been recognized as an important platform chemical that can be produced from biomass. While a number of organisms are capable of succinate production naturally, this review focuses on the engineering of Escherichia coli for the production of four-carbon dicarboxylic acid. Important features of a succinate production system are to achieve an optimal balance of reducing equivalents generated by consumption of the feedstock, while maximizing the amount of carbon channeled into the product. Aerobic and anaerobic production strains have been developed and applied to production from glucose and other abundant carbon sources. Metabolic engineering methods and strain evolution have been used and supplemented by the recent application of systems biology and in silico modeling tools to construct optimal production strains. The metabolic capacity of the production strain, the requirement for efficient recovery of succinate, and the reliability of the performance under scaleup are important in the overall process. The costs of the overall biorefinery-compatible process will determine the economic commercialization of succinate and its impact in larger chemical markets.

Ethanol production from marine algal hydrolysates using Escherichia coli KO11

Algae biomass is a potential raw material for the production of biofuels and other chemicals. In this study, biomass of the marine algae, Ulva lactuca, Gelidium amansii,Laminaria japonica, and Sargassum fulvellum, was treated with acid and commercially available hydrolytic enzymes. The hydrolysates contained glucose, mannose, galactose, and mannitol, among other sugars, at different ratios. The Laminaria japonica hydrolysate contained up to 30.5% mannitol and 6.98% glucose in the hydrolysate solids. Ethanogenic recombinant Escherichia coli KO11 was able to utilize both mannitol and glucose and produced 0.4g ethanol per g of carbohydrate when cultured in L. japonica hydrolysate supplemented with Luria-Bertani medium and hydrolytic enzymes. The strategy of acid hydrolysis followed by simultaneous enzyme treatment and inoculation with E. coli KO11 could be a viable strategy to produce ethanol from marine alga biomass.

A complete industrial system for economical succinic acid production by Actinobacillus succinogenes

An industrial fermentation system using lignocellulosic hydrolysate, waste yeast hydrolysate, and mixed alkali to achieve high-yield, economical succinic acid production by Actinobacillus succinogenes was developed. Lignocellulosic hydrolysate and waste yeast hydrolysate were used efficiently as carbon sources and nitrogen source instead of the expensive glucose and yeast extract. Moreover, as a novel method for regulating pH mixed alkalis (Mg(OH)(2) and NaOH) were first used to replace the expensive MgCO(3) for succinic acid production. Using the three aforementioned substitutions, the total fermentation cost decreased by 55.9%, and 56.4 g/L succinic acid with yield of 0.73 g/g was obtained, which are almost the same production level as fermentation with glucose, yeast extract and MgCO(3). Therefore, the cheap carbon and nitrogen sources, as well as the mixed alkaline neutralize could be efficiently used instead of expensive composition for industrial succinic acid production.

Production of ε-poly-L: -lysine using a novel two-stage pH control strategy by Streptomyces sp. M-Z18 from glycerol

The production of ε-poly-L: -lysine (ε-PL) by Streptomyces sp. M-Z18 from glycerol was investigated in a 5-L jar-fermenter. Batch fermentations by Streptomyces sp. M-Z18 at various pH values ranging from 3.5 to 4.5 were studied. Based on the analysis of the time course of specific cell growth rate and specific ε-PL formation rate, a novel two-stage pH control strategy was developed to improve ε-PL production by shifting the culture pH from 3.5 to 3.8 after 36 h of cultivation. By applying the strategy, the maximal ε-PL concentration and productivity had a significant improvement and reached 9.13 g L(-1) and 4.76 g L(-1) day(-1), respectively, compared with those in one-stage pH control process where the pH value is controlled at 3.5 (7.83 g L(-1) and 3.13 g L(-1) day(-1)). Fed-batch fermentation with two-stage pH control strategy was also applied to produce ε-PL; final ε-PL concentration of 30.11 g L(-1) was obtained, being 3.3-fold greater than that of batch fermentation. To our knowledge, it is the first report on production of ε-PL from glycerol in fermenter scale and achievement of high ε-PL production with two-stage pH control strategy.