Industrial biotechnology for the production of bio-based chemicals – a cradle-to-grave perspective

Knowledge management in a waste based biorefinery in the QbD paradigm

Shifting resource base from fossil feedstock to renewable raw materials for production of chemical products has opened up an area of novel applications of industrial biotechnology-based process tools. This review aims to provide a concise and focused discussion on recent advances in knowledge management to facilitate efficient and optimal operation of a biorefinery. Application of quality by design (QbD) and process analytical technology (PAT) as tools for knowledge creation and management at different levels has been highlighted. Role of process integration, government policies, knowledge exchange through collaboration, and use of databases and computational tools have also been touched upon.

Enzymatic production of 5'-inosinic acid by AMP deaminase from a newly isolated Aspergillus oryzae

5'-adenylic acid deaminase (AMP deaminase), an important enzyme for the food industry, can catalyze the irreversible hydrolysis of adenosine monophosphate (AMP) to inosine monophosphate (IMP) and ammonia. In this study, a new strain was screened that efficiently produces 3191.6U/g of AMP deaminase at 32°C. After purification, the optimal temperature and pH of the AMP deaminase were found to be 40°C and 6.0, respectively, but it was partially inhibited by Fe(3+), Cu(2+), Al(3+), and Zn(2+). With amplification of the AMP deaminase production system, 6mL of crude enzyme could produce 2.00mg/g of IMP from 2.04mg/g of dried yeast with an 84.8% molar yield after 40min. These results provide a new insight into AMP deaminase production and offer a potential platform for producing 5'-IMP.

Selective oxidation of trimethylolpropane to 2,2-bis(hydroxymethyl)butyric acid using growing cells of Corynebacterium sp. ATCC 21245

Multifunctional chemicals including hydroxycarboxylic acids are gaining increasing interest due to their growing applications in the polymer industry. One approach for their production is a biological selective oxidation of polyols, which is difficult to achieve by conventional chemical catalysis. In the present study, trimethylolpropane (TMP), a trihydric alcohol, was subjected to selective oxidation using growing cells of Corynebacterium sp. ATCC 21245 as a biocatalyst and yielding the dihydroxy-monocarboxylic acid, 2,2-bis(hydroxymethyl)butyric acid (BHMB). The study revealed that co-substrates are crucial for this reaction. Among the different evaluated co-substrates, a mixture of glucose, xylose and acetate at a ratio of 5:5:2 was found optimum. The optimal conditions for biotransformation were pH 8, 1v/v/m airflow and 500rpm stirring speed. In batch mode of operation, 70.6% of 5g/l TMP was converted to BHMB in 10 days. For recovery of the product the adsorption pattern of BHMB to the anion exchange resin, Ambersep(®) 900 (OH(-)), was investigated in batch and column experiments giving maximum static and dynamic binding capacities of 135 and 144mg/g resin, respectively. BHMB was separated with 89.7% of recovery yield from the fermentation broth. The approach is applicable for selective oxidation of other highly branched polyols by biotransformation.

Synthesis of Octyl-β-Glucoside Catalyzed by Almond β-Glucosidase in Unconventional Reaction Media

The reaction system for octyl-β-glucoside synthesis catalysed by the almond-β-glucosidase has been characterised. The monophasic octanol saturated with different amounts of water served as a reaction medium. Both the glucose and the activated substrate p-nitrophenyl-β-glucoside were examined as glycon donors. The reverse hydrolysis and the transglycosylation were both used as reaction models for this enzymatically catalysed alkyl-β-glucoside synthesis. The rate of synthesis of octyl-β-glucoside (v_S), the rate of hydrolysis, i.e. the glucose formation (v_H) and the predicted yield (Y) were determined. The effect of water activity on the synthetic and hydrolytic activity of the enzyme was investigated. Both the rate of synthesis and the rate of hydrolysis increased with the increase of the water activity in the reaction system, showing their maximum values at the water activity close to the saturation level. Thus, the maximum ratio of v_S/v_H=0.165 was achieved at the water activity of 0.94. The predicted yields were 0.5, 0.75 and 14.19% and were lower than the actually achieved yields of 19.45, 38 and 36.40% at the water activities of 0.75, 0.84 and 0.94, respectively. The yield of octyl-β-glucoside in the reverse hydrolysis was only 15.2%, i.e. 3.25 times lower than the yield obtained in the transglycosylation reaction with the water activity of 0.94. The solubility of glucose in pure octanol was only 1.5 mmol/L at the saturation level of 12 mmol/L in the presence of 10 mmol/L of p-nitrophenyl-β-glucoside, and it increased to 15.5 mmol/L in the presence of octyl-β-glucoside.

Enhanced succinic acid production in Aspergillus saccharolyticus by heterologous expression of fumarate reductase from Trypanosoma brucei

Aspergillus saccharolyticus exhibits great potential as a cell factory for industrial production of dicarboxylic acids. In the analysis of the organic acid profile, A. saccharolyticus was cultivated in an acid production medium using two different pH conditions. The specific activities of the enzymes, pyruvate carboxylase (PYC), malate dehydrogenase (MDH), and fumarase (FUM), involved in the reductive tricarboxylic acid (rTCA) branch, were examined and compared in cells harvested from the acid production medium and a complete medium. The results showed that ambient pH had a significant impact on the pattern and the amount of organic acids produced by A. saccharolyticus. The wild-type strain produced higher amount of malic acid and succinic acid in the pH buffered condition (pH 6.5) compared with the pH non-buffered condition. The enzyme assays showed that the rTCA branch was active in the acid production medium as well as the complete medium, but the measured enzyme activities were different depending on the media. Furthermore, a soluble NADH-dependent fumarate reductase gene (frd) from Trypanosoma brucei was inserted and expressed in A. saccharolyticus. The expression of the frd gene led to an enhanced production of succinic acid in frd transformants compared with the wild-type in both pH buffered and pH non-buffered conditions with highest amount produced in the pH buffered condition (16.2 ± 0.5 g/L). This study demonstrates the feasibility of increasing succinic acid production through the cytosolic reductive pathway by genetic engineering in A. saccharolyticus.

Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor

The success of biotechnological processes is based on the availability of efficient and highly specific biocatalysts, which can satisfy industrial demands. Extreme and remote environments like the deep brine pools of the Red Sea represent highly interesting habitats for the discovery of novel halophilic and thermophilic enzymes. Haloferax volcanii constitutes a suitable expression system for halophilic enzymes obtained from such brine pools. We developed a batch process for the cultivation of H. volcanii H1895 in controlled stirred-tank bioreactors utilising knockouts of components of the flagella assembly system. The standard medium Hv-YPC was supplemented to reach a higher cell density. Without protein expression, cell dry weight reaches 10 g L(-1). Two halophilic alcohol dehydrogenases were expressed under the control of the tryptophanase promoter p.tna with 16.8 and 3.2 mg gCDW (-1), respectively, at a maximum cell dry weight of 6.5 g L(-1). Protein expression was induced by the addition of L-tryptophan. Investigation of various expression strategies leads to an optimised two-step induction protocol introducing 6 mM L-tryptophan at an OD650 of 0.4 followed by incubation for 16 h and a second induction step with 3 mM L-tryptophan followed by a final incubation time of 4 h. Compared with the uncontrolled shaker-flask cultivations used until date, dry cell mass concentrations were improved by a factor of more than 5 and cell-specific enzyme activities showed an up to 28-fold increased yield of the heterologous proteins.

Purification and simultaneous immobilization of Arabidopsis thaliana hydroxynitrile lyase using a family 2 carbohydrate-binding module

Tedious, time- and labor-intensive protein purification and immobilization procedures still represent a major bottleneck limiting the widespread application of enzymes in synthetic chemistry and industry. We here exemplify a simple strategy for the direct site-specific immobilization of proteins from crude cell extracts by fusion of a family 2 carbohydrate-binding module (CBM) derived from the exoglucanase/xylanase Cex from Cellulomonas fimi to a target enzyme. By employing a tripartite fusion protein consisting of the CBM, a flavin-based fluorescent protein (FbFP), and the Arabidopsis thaliana hydroxynitrile lyase (AtHNL), binding to cellulosic carrier materials can easily be monitored via FbFP fluorescence. Adsorption properties (kinetics and quantities) were studied for commercially available Avicel PH-101 and regenerated amorphous cellulose (RAC) derived from Avicel. The resulting immobilizates showed similar activities as the wild-type enzyme but displayed increased stability in the weakly acidic pH range. Finally, Avicel, RAC and cellulose acetate (CA) preparations were used for the synthesis of (R)-mandelonitrile in micro-aqueous methyl tert-butyl ether (MTBE) demonstrating the applicability and stability of the immobilizates for biotransformations in both aqueous and organic reaction systems.

Eco-dialysis: the financial and ecological costs of dialysis waste products: is a 'cradle-to-cradle' model feasible for planet-friendly haemodialysis waste management?

BACKGROUND

Approximately 2 million chronic haemodialysis patients produce over 2,000,000 tons of waste per year that includes about 600,000 tons of potentially hazardous waste. The aim of the present study was to analyse the characteristics of the waste that is produced through chronic haemodialysis in an effort to identify strategies to reduce its environmental and financial impact.

METHODS

The study included three dialysis machines and disposables for bicarbonate dialysis, haemodiafiltration (HFR) and lactate dialysis. Hazardous waste is defined as waste that comes into contact with bodily fluids. The weight and cost of waste management was evaluated by various policies of differentiation, ranging from a careful-optimal differentiation to a careless one. The amount of time needed for optimal management was recorded in 30 dialysis sessions. Non-hazardous materials were assessed for potential recycling.

RESULTS

The amount of plastic waste that is produced per dialysis session ranges from 1.5 to 8 kg (from 1.1 to 8 kg of potentially hazardous waste), depending upon the type of dialysis machine and supplies, differentiation and emptying policies. The financial cost of waste disposal is high, and is mainly related to hazardous waste disposal, with costs ranging from 2.2 to 16 Euro per session (2.7-21 USD) depending on the waste management policy. The average amount of time needed for careful, optimal differentiation disposal is approximately 1 minute for a haemodialysis session and 2 minutes for HFR. The ecological cost is likewise high: less than one-third of non-hazardous waste (23-28%) is potentially recyclable, while the use of different types of plastic, glues, inks and labels prevents the remaining materials from being recycled.

CONCLUSION

Acknowledging the problem of waste management in dialysis could lead to savings of hundreds of millions of Dollars and to the reuse and recycling of hundreds of tons of plastic waste per year on a world-wide scale with considerable financial and ecological savings.

Microbial production of Propionic and Succinic acid from Sorbitol using Propionibacterium acidipropionici

Three sequential fermentative batches were carried out with cell recycle in four simultaneously operating bioreactors maintained at pH 6.5, 30°C, and 100 rpm. P. acidipropionici ATCC 4875 was able to produce propionic and succinic acid from sorbitol. The concentration of propionic acid decreased slightly from 39.5 ± 5.2 g L⁻¹ to 34.4 ± 1.9 g L⁻¹, and that of succinic acid increased significantly from 6.1 ± 2.1 g L⁻¹ to 14.8 ± 0.9 g L⁻¹ through the sequential batches. In addition, a small amount of acetic acid was produced that decreased from 3.3 ± 0.4 g L⁻¹ to 2.0 ± 0.3 g L⁻¹ through the batches. The major yield for propionic acid was 0.613 g g⁻¹ in the first batch and succinic acid it was 0.212 g g⁻¹ in the third batch. The minor yield of acetic acid was 0.029 g g⁻¹, in the second and third batches.

Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome

Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (∼5). Hydrogen production by biocathodes poised at −600 mV vs. SHE increased>100-fold and acetate production ceased at acidic pH, but ∼5–15 mM (catholyte volume)/day acetate and>1,000 mM/day hydrogen were attained at pH ∼6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm² at −765 mV (0.065 mA/cm² sterile control at −800 mV) by the Acetobacterium-dominated community. Supplying −800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m³/day hydrogen (≈2.6 gallons gasoline equivalent), 0.7 kg/m³/day formate, and 3.1 kg/m³/day acetate ( = 4.7 kg CO₂ captured).

A novel whole-phase succinate fermentation strategy with high volumetric productivity in engineered Escherichia coli

The strategic design of this study aims at fermentative succinate production with high volumetric productivity in engineered Escherichia coli. An E. coli YL106/pSCsfcA was engineered to produce succinate under aerobic, microaerobic and anaerobic conditions by derepressing the inhibition of low dissolved oxygen, eliminating the NADH competitive pathways, modulating the redistribution of metabolic flux, and increasing the transport rate of the sole carbon source glucose. Based on this strain, a novel "whole-phase" succinate production strategy was further developed, in which the engineered strain was first cultivated aerobically, then shifted to microaerobic phase at the end of exponential growth, and finally kept in anaerobic phase until the end of fermentation. Employing this strategy, the engineered E. coli YL106/pSCsfcA was able to produce 85.30 g l(-1) succinate with an overall volumetric productivity of 2.13 g l(-1)h(-1). This process offers an efficiently fermentative method for industrial succinate production in metabolically engineered E. coli.

In silico aided metabolic engineering of Klebsiella oxytoca and fermentation optimization for enhanced 2,3-butanediol production

Klebsiella oxytoca naturally produces a large amount of 2,3-butanediol (2,3-BD), a promising bulk chemical with wide industrial applications, along with various byproducts. In this study, the in silico gene knockout simulation of K. oxytoca was carried out for 2,3-BD overproduction by inhibiting the formation of byproducts. The knockouts of ldhA and pflB genes were targeted with the criteria of maximization of 2,3-BD production and minimization of byproducts formation. The constructed K. oxytoca ΔldhA ΔpflB strain showed higher 2,3-BD yields and higher final concentrations than those obtained from the wild-type and ΔldhA strains. However, the simultaneous deletion of both genes caused about a 50 % reduction in 2,3-BD productivity compared with K. oxytoca ΔldhA strain. Based on previous studies and in silico investigation that the agitation speed during 2,3-BD fermentation strongly affected cell growth and 2,3-BD synthesis, the effect of agitation speed on 2,3-BD production was investigated from 150 to 450 rpm in 5-L bioreactors containing 3-L culture media. The highest 2,3-BD productivity (2.7 g/L/h) was obtained at 450 rpm in batch fermentation. Considering the inhibition of acetoin for 2,3-BD production, fed-batch fermentations were performed using K. oxytoca ΔldhA ΔpflB strain to enhance 2,3-BD production. Altering the agitation speed from 450 to 350 rpm at nearly 10 g/L of acetoin during the fed-batch fermentation allowed for the production of 113 g/L 2,3-BD, with a yield of 0.45 g/g, and for the production of 2.1 g/L/h of 2,3-BD.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Genome sequence of Pseudomonas putida S12, a potential platform strain for industrial production of valuable chemicals

Pseudomonas putida strain S12, a well-studied solvent-tolerant bacterium, is considered a platform strain for the production of many chemicals. Here, we present a 6.28-Mb assembly of its genome sequence. We have annotated 32 coding sequences (CDSs) encoding efflux systems of organic compounds and 195 CDSs responsible for the metabolism of aromatic compounds.

Genome-scale model management and comparison

Spurred by recent innovations in genome sequencing, the reconstruction of genome-scale models has increased in recent years. Genome-scale models are now available for a wide range of organisms, and models have been successfully applied to a number of research topics including metabolic engineering, genome annotation, biofuel production, and interpretation of omics data sets. The challenge is how to manage the large amount of data in genome-scale models and perform comparative analysis to gain new biological insights. In this chapter, important standards for genome-scale modeling are outlined. Furthermore, management strategies as well as existing repository and construction tools are discussed. As the comparison of models is an important aspect during the development and analysis stages, available methods are presented and existing software solutions are reviewed.

Synthesis of chiral cyanohydrins by recombinant Escherichia coli cells in a micro-aqueous reaction system

Synthesis of chiral cyanohydrins is performed in a monophasic micro-aqueous reaction system using whole recombinant Escherichia coli cells expressing the Arabidopsis thaliana hydroxynitrile lyase (AtHNL). Microscopy studies employing a fusion of AtHNL with a flavin-based fluorescent protein (FbFP) reveal that the cells remain intact in the reaction system.

A limited LCA of bio-adipic acid: manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks

A limited life cycle assessment (LCA) was performed on a combined biological and chemical process for the production of adipic acid, which was compared to the traditional petrochemical process. The LCA comprises the biological conversion of the aromatic feedstocks benzoic acid, impure aromatics, toluene, or phenol from lignin to cis, cis-muconic acid, which is subsequently converted to adipic acid through hydrogenation. Apart from the impact of usage of petrochemical and biomass-based feedstocks, the environmental impact of the final concentration of cis, cis-muconic acid in the fermentation broth was studied using 1.85% and 4.26% cis, cis-muconic acid. The LCA focused on the cumulative energy demand (CED), cumulative exergy demand (CExD), and the CO(2) equivalent (CO(2) eq) emission, with CO(2) and N(2) O measured separately. The highest calculated reduction potential of CED and CExD were achieved using phenol, which reduced the CED by 29% and 57% with 1.85% and 4.26% cis, cis-muconic acid, respectively. A decrease in the CO(2) eq emission was especially achieved when the N(2) O emission in the combined biological and chemical process was restricted. At 4.26% cis, cis-muconic acid, the different carbon backbone feedstocks contributed to an optimized reduction of CO(2) eq emissions ranging from 14.0 to 17.4 ton CO(2) eq/ton adipic acid. The bulk of the bioprocessing energy intensity is attributed to the hydrogenation reactor, which has a high environmental impact and a direct relationship with the product concentration in the broth.

Microbial 2,3-butanediol production: a state-of-the-art review

2,3-butanediol is a promising bulk chemical due to its extensive industry applications. The state-of-the-art nature of microbial 2,3-butanediol production is reviewed in this paper. Various strategies for efficient and economical microbial 2,3-butanediol production, including strain improvement, substrate alternation, and process development, are reviewed and compared with regard to their pros and cons. This review also summarizes value added derivatives of biologically produced 2,3-butanediol and different strategies for downstream processing. The future prospects of microbial 2,3-butanediol production are discussed in light of the current progress, challenges, and trends in this field. Guidelines for future studies are also proposed.

Extension of the substrate utilization range of Ralstonia eutropha strain H16 by metabolic engineering to include mannose and glucose

The gram-negative facultative chemolithoautotrophic bacterium Ralstonia eutropha strain H16 is known for its narrow carbohydrate utilization range, which limits its use for biotechnological production of polyhydroxyalkanoates and possibly other products from renewable resources. To broaden its substrate utilization range, which is for carbohydrates and related compounds limited to fructose, N-acetylglucosamine, and gluconate, strain H16 was engineered to use mannose and glucose as sole carbon sources for growth. The genes for a facilitated diffusion protein (glf) from Zymomonas mobilis and for a glucokinase (glk), mannofructokinase (mak), and phosphomannose isomerase (pmi) from Escherichia coli were alone or in combination constitutively expressed in R. eutropha strain H16 under the control of the neokanamycin or lac promoter, respectively, using an episomal broad-host-range vector. Recombinant strains harboring pBBR1MCS-3::glf::mak::pmi or pBBR1MCS-3::glf::pmi grew on mannose, whereas pBBR1MCS-3::glf::mak and pBBR1MCS-3::glf did not confer the ability to utilize mannose as a carbon source to R. eutropha. The recombinant strain harboring pBBR1MCS-3::glf::pmi exhibited slower growth on mannose than the recombinant strain harboring pBBR1MCS-3::glf::mak::pmi. These data indicated that phosphomannose isomerase is required to convert mannose-6-phosphate into fructose-6-phosphate for subsequent catabolism via the Entner-Doudoroff pathway. In addition, all plasmids also conferred to R. eutropha the ability to grow in the presence of glucose. The best growth was observed with a recombinant R. eutropha strain harboring plasmid pBBR1MCS-2::P(nk)::glk::glf. In addition, expression of the respective enzymes was demonstrated at the transcriptional and protein levels and by measuring the activities of mannofructokinase (0.622 ± 0.063 U mg(-1)), phosphomannose isomerase (0.251 ± 0.017 U mg(-1)), and glucokinase (0.518 ± 0.040 U mg(-1)). Cells of recombinant strains of R. eutropha synthesized poly(3-hydroxybutyrate) to ca. 65 to 67% (wt/wt) of the cell dry mass in the presence of 1% (wt/vol) glucose or mannose as the sole carbon sources.

A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products

In the last decade, there has been increasing research interest in the value of bio-sourced materials recovered from residual biomass. Research that focuses on the use of extracted, recovered and/or synthesized bioproducts for direct industrial applications is essential for the implementation of sustainable approaches in a forward-looking bio-based economy. The effective use of biomass feedstocks, particularly lignocellulosic materials (plant biomass predominantly comprised of cellulose, hemicellulose, and lignin), in large-scale applications will evolve from innovative research aimed at the development and implementation of biorefineries--multi-step, multi-product facilities established for specific bio-sourced feedstocks. This paper presents recent advances in lignocellulosic biomass processing and analysis from a biorefining perspective. In addition, existing industrial biomass processing applications are discussed and examined within a biorefinery context.

Metabolic engineering of Escherichia coli for biotechnological production of high-value organic acids and alcohols

Confronted with the gradual and inescapable exhaustion of the earth's fossil energy resources, the bio-based process to produce platform chemicals from renewable carbohydrates is attracting growing interest. Escherichia coli has been chosen as a workhouse for the production of many valuable chemicals due to its clear genetic background, convenient to be genetically modified and good growth properties with low nutrient requirements. Rational strain development of E. coli achieved by metabolic engineering strategies has provided new processes for efficiently biotechnological production of various high-value chemical building blocks. Compared to previous reviews, this review focuses on recent advances in metabolic engineering of the industrial model bacteria E. coli that lead to efficient recombinant biocatalysts for the production of high-value organic acids like succinic acid, lactic acid, 3-hydroxypropanoic acid and glucaric acid as well as alcohols like 1,3-propanediol, xylitol, mannitol, and glycerol with the discussion of the future research in this area. Besides, this review also discusses several platform chemicals, including fumaric acid, aspartic acid, glutamic acid, sorbitol, itaconic acid, and 2,5-furan dicarboxylic acid, which have not been produced by E. coli until now.