Glycerol assimilation and production of 1,3-propanediol by Citrobacter amalonaticus Y19

Progress in 1,3-propanediol biosynthesis

1,3-Propanediol (1,3-PDO) is one of the important organic chemical materials and is widely used in polyester synthesis, and it also shows great potential in medicine, cosmetics, resins, and biodegradable plastics. So far, 1,3-PDO mainly comes from chemical synthesis. However, the by-products and the side effects during chemical synthesis of 1,3-PDO bring about serious damage to the environment. In recent years, the biosynthetic pathway of 1,3-PDO has been elucidated in microorganisms. Under the action of glycerol dehydratase (GDHt) and propanediol oxidoreductase (PDOR), glycerol can be catalyzed to form 1,3-PDO through the reduction pathway. Compared to the chemical synthesis, the biosynthesis of 1,3-PDO is environmentally friendly but would face the problem of low production. To improve the yield, the native 1,3-PDO producing strains have been modified by genetic engineering, and the biosynthetic pathway has been reconstructed in the model microorganism, Escherichia coli. In this review, we summarize the research progress of the 1,3-PDO biosynthesis in microorganisms, and hopefully, it will provide reference for the renewable production of 1,3-PDO in industry.

Enhanced 1,3-propanediol production with high yield from glycerol through a novel Klebsiella-Shewanella co-culture

BACKGROUND

1,3-Propanediol (1,3-PDO) is a platform compound, which has been widely used in food, pharmaceutical and cosmetic industries. Compared with chemical methods, the biological synthesis of 1,3-PDO has shown promising applications owing to its mild conditions and environmental friendliness. However, the biological synthesis of 1,3-PDO still has the problem of low titer and yield due to the shortage of reducing powers.

RESULTS

In this study, Klebsiella sp. strain YT7 was successfully isolated, which can synthesize 11.30 g/L of 1,3-PDO from glycerol in flasks. The intracellular redox regulation strategy based on the addition of electron mediators can increase the 1,3-PDO titer to 28.01 g/L. Furthermore, a co-culturing system consisting of strain YT7 and Shewanella oneidensis MR-1 was established, which can eliminate the supplementation of exogenous electron mediators and reduce the by-products accumulation. The 1,3-PDO yield reached 0.44 g/g and the final titer reached 62.90 g/L. The increased titer and yield were attributed to the increased redox levels and the consumption of by-products.

CONCLUSIONS

A two-bacterium co-culture system with Klebsiella sp. strain YT7 and S. oneidensis strain MR-1 was established, which realized the substitution of exogenous electron mediators and the reduction of by-product accumulation. Results provided theoretical basis for the high titer of 1,3-PDO production with low by-product concentration.

An overview on the conversion of glycerol to value-added industrial products via chemical and biochemical routes

Glycerol is a common by-product of industrial biodiesel syntheses. Due to its properties, availability, and versatility, residual glycerol can be used as a raw material in the production of high value-added industrial inputs and outputs. In particular, products like hydrogen, propylene glycol, acrolein, epichlorohydrin, dioxalane and dioxane, glycerol carbonate, n-butanol, citric acid, ethanol, butanol, propionic acid, (mono-, di-, and triacylglycerols), cynamoil esters, glycerol acetate, benzoic acid, and other applications. In this context, the present study presents a critical evaluation of the innovative technologies based on the use of residual glycerol in different industries, including the pharmaceutical, textile, food, cosmetic, and energy sectors. Chemical and biochemical catalysts in the transformation of residual glycerol are explored, along with the factors to be considered regarding the choice of catalyst route used in the conversion process, aiming at improving the production of these industrial products.

Isolation and characterization of a newly identified Clostridium butyricum strain SCUT343-4 for 1,3-propanediol production

A novel 1,3-propanediol (1,3-PDO) producing strain was isolated and identified as Clostridium butyricum with respect to its morphological and physiological characteristics, as well as 16S rDNA. The results of substrates test and stress tolerance indicated that C. butyricum SCUT343-4 could produce 1,3-PDO efficiently from glycerol. The optimal fermentation conditions were determined to be 5 g/L yeast extract at 37 °C and pH 6.5. To fully evaluate its 1,3-PDO production capacity, different cultivation strategies have been implemented. The highest 1,3-PDO concentration obtained for batch and fed-batch fermentation were 51.64 and 61.30 g/L, respectively. Immobilized cell fermentation in fibrous-bed bioreactor was also performed, and the concentration of 1,3-PDO further increased to 86 g/L with a yield of 0.52 g/g. In addition, the 1,3-PDO productivity reached 4.20 g/L h, which is the highest level reported for C. butyricum, demonstrating the potential of C. butyricum SCUT343-4 for 1,3-PDO production from glycerol.

Engineering Escherichia coli for Direct Production of 1,2-Propanediol and 1,3-Propanediol from Starch

Diols are versatile chemicals used for multiple manufacturing products. In some previous studies, Escherichia coli has been engineered to produce 1,2-propanediol (1,2-PDO) and 1,3-propanediol (1,3-PDO) from glucose. However, there are no reports on the direct production of these diols from starch instead of glucose as a substrate. In this study, we directly produced 1,2-PDO and 1,3-PDO from starch using E. coli engineered for expressing a heterologous α-amylase, along with the expression of 1,2-PDO and 1,3-PDO synthetic genes. For this, the recombinant plasmids, pVUB3-SBA harboring amyA gene for α-amylase production, pSR5 harboring pct, pduP, and yahK genes for 1,2-PDO production, and pSR8 harboring gpd1-gpp2, dhaB123, gdrAB, and dhaT genes for 1,3-PDO production, were constructed. Subsequently, E. coli BW25113 (ΔpflA) and BW25113 strains were transformed with pVUB3-SBA, pSR5, and/or pSR8. Using these transformants, direct production of 1,2-PDO and 1,3-PDO from starch was demonstrated under microaerobic condition. As a result, the maximum production titers of 1,2-PDO and 1,3-PDO from 1% glucose as a sole carbon source were 13 mg/L and 150 mg/L, respectively. The maximum production titers from 1% starch were similar levels (30 mg/L 1,2-PDO and 120 mg/L 1,3-PDO). These data indicate that starch can be an alternative carbon source for the production of 1,2-PDO and 1,3-PDO in engineered E. coli. This technology could simplify the upstream process of diol bioproduction.

Small Current but Highly Productive Synthesis of 1,3-Propanediol from Glycerol by an Electrode-Driven Metabolic Shift in Klebsiella pneumoniae L17

Electrofermentation actively regulates the bacterial redox state, which is essential for bioconversion and has been highlighted as an effective method for further improvements of the productivity of either reduced or oxidized platform chemicals. 1,3-Propanediol (1,3-PDO) is an industrial value-added chemical that can be produced from glycerol fermentation. The bioconversion of 1,3-PDO from glycerol requires additional reducing energy under anoxic conditions. The cathode-based conversion of glycerol to 1,3-PDO with various electron shuttles (2-hydroxy-1,4-naphthoquinone, neutral red, and hydroquinone) using Klebsiella pneumoniae L17 was investigated. The externally poised potential of -0.9 V vs. Ag/AgCl to the cathode increased 1,3-PDO (35.5±3.1 mm) production if 100 μm neutral red was used compared with non-bioelectrochemical system fermentation (23.7±2.4 mm). Stoichiometric metabolic flux and transcriptional analysis indicated a shift in the carbon flux toward the glycerol reductive pathway. The homologous overexpression of glycerol dehydratase (DhaB) and 1,3-PDO oxidoreductase (DhaT) enzymes synergistically enhanced 1,3-PDO conversion (39.3±0.8 mm) under cathode-driven fermentation. Interestingly, a small current uptake (0.23 mmol of electrons) caused significant metabolic flux changes with a concomitant increase in 1,3-PDO production. This suggests that both an increase in 1,3-PDO production and regulation of the cellular metabolic pathway are feasible by electrode-driven control in cathodic electrofermentation.

Monitoring steady production of 1,3-propanediol during bioprospecting of glycerol-assimilating soil microbiome using dye-based pH-stat method

AIM

In this investigation, a dye-based pH-stat method was devised for monitoring steady production of 1,3-propanediol (1,3-PDO) during bioprospecting of glycerol-assimilating soil microbiome.

METHODS AND RESULTS

Soil samples were collected from two potential sites of CSIR-IIP, India. Selective enrichment of microbial consortia was done using the glycerol-based medium at initial stage, followed by purification to isolated colonies, after positive high-performance liquid chromatography detection of 1,3-PDO in the fermentation broth. When the purified isolated were re-tested for 1,3-PDO production, only two isolates namely Isolate 1 and Isolate 3 were capable of producing the targeted product preferably under anaerobic conditions. Based on better 1,3-PDO fermentation efficiency (Isolate 3, 22% vs Isolate 1, 4·48%) and acetic acid as the only major by-product, Isolate 3 was shortlisted for further studies. A dye-based technique was devised in which bromothymol blue was incorporated into the medium to monitor the pH drop due to acetic acid formation and hence change in colour. Visual change in colour helped in intermittent pH restoration. During fermentation, with pH stat being 8-8·5, Isolate 3 at 32°C yielded 0·67 mol mol^-1 1,3-PDO within a short span of 12 h only with an initial concentration of glycerol being 20 g l^-1 . Phylogenetic analysis revealed that Isolate 3 shared 95·8% homology with Citrobacter freundii CFNIH1 and hence designated as C. freundii IIP DR3.

CONCLUSION

This study demonstrated that during bioprospecting glycerol-assimilating microbiome, dye-based technique can be successfully employed. This technique can further be exploited to monitor consistent production of all microbial secondary metabolites that accompanies acid production.

SIGNIFICANCE AND IMPACT OF THE STUDY

Incorporation of 'Bromothymol blue' can visually help in the identification of pH drop in the medium, so that pH stat can be easily maintained during 1,3-PDO production from glycerol especially under shake flask conditions.

Metabolic engineering of Klebsiella pneumoniae J2B for the production of 1,3-propanediol from glucose

The production of 1,3-propanediol (1,3-PDO) from glucose was investigated using Klebsiella pneumoniae J2B, which converts glycerol to 1,3-PDO and synthesize an essential coenzyme B₁₂. In order to connect the glycolytic pathway with the pathway of 1,3-PDO synthesis from glycerol, i.e., to directly produce diol from glucose, glycerol-3-phosphate dehydrogenase and glycerol-3-phosphate phosphatase from Saccharomyces cerevisiae were overexpressed. Additionally, the effect of expression levels and the use of isoforms of these two enzymes on glycerol and 1,3-PDO production were studied. Furthermore, to prevent loss of produced glycerol, the glycerol oxidation pathways were disrupted. Finally, the conversion rate of glycerol to 1,3-PDO was increased via homologous overexpression of glycerol dehydratase and 1,3-PDO oxidoreductase. The resultant strain successfully produced 1,3-PDO from glucose at a yield of 0.27mol/mol along with glycerol at 0.52mol/mol. Improvement of the engineered K. pneumoniae J2B to further increase conversion of glycerol to 1,3-PDO is discussed.

CATALOGIC 301C model - validation and improvement

In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL. CATALOGIC 301C model meets all REACH requirements to be used for biodegradability assessment. The model formalism built on scientific understanding for the microbial degradation of chemicals has a well-defined and transparent applicability domain. The model predictions are adequate for the evaluation of the ready degradability of chemicals.

Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis

3-hydroxypropionaldehyde (3-HPA) and 1,3-propanediol (1,3-PD) are subproducts of glycerol degradation and of economical interest as they are used for polymers synthesis, such as polyesters and polyurethanes. Some few characterized bacterial species (mostly from Firmicutes and Gamma-proteobacteria groups) are able to catabolize these monomers from glycerol using the gene products from the dha regulon. To expand our knowledge and direct further experimental studies on the regulon and related genes for the anaerobic glycerol metabolism, an extensive genomic screening was performed to identify the presence of the dha genes in fully sequenced prokaryotic genomes. Interestingly, this work shows that although only few bacteria species are known to produce 3-HPA or 1,3-PD, the incomplete regulon is found in more than 100 prokaryotic genomes. However, the complete pathway is found only in a few dozen species belonging to five different taxonomic groups, including one Archaea species, Halalkalicoccus jeotgali. Phylogenetic analysis and conservation of both gene synteny and primary sequence similarity reinforce the idea that these genes have a common origin and were possibly acquired by lateral gene transfer (LGT). Besides the evolutionary aspect, the identification of homologs from several different organisms may predict potential alternative targets for faster or more efficient biological synthesis of 3-HPA or 1,3-PD.

Complete genome sequence of novel carbon monoxide oxidizing bacteria Citrobacter amalonaticus Y19, assembled de novo

We report here the complete genome sequence of Citrobacter amalonaticus Y19 isolated from an anaerobic digester. PacBio single-molecule real-time (SMRT) sequencing was employed, resulting in a single scaffold of 5.58Mb. The sequence of a mega plasmid of 291Kb size is also presented.

Dual synthetic pathway for 3-hydroxypropionic acid production in engineered Escherichia coli

3-Hydroxypropionic acid (3-HP) is an important platform C3 chemical; production of 3-HP in recombinant Escherichia coli by synthetic pathways has been the focus of a lot of research. When glycerol is used as a substrate to produce 3-HP in E. coli, only the ALDH pathway (employing aldehyde dehydrogenase (ALDH) for conversion of 3-hydroxypropionaldehyde (3-HPA) into 3-HP) has been utilized as a synthetic pathway. However, several bacteria (including Klebsiella pneumoniae) are known to have the ability to produce 3-HP by the Pdu pathway (employing the PduP, PduL, and PduW enzymes). Here, we report the production of 3-HP in E. coli by using the Pdu pathway from K. pneumoniae as a synthetic pathway. Moreover, a strain harboring a dual synthetic pathways (ALDH and Pdu) exhibited a 70% increase in 3-HP titer compared to one harboring the ALDH pathway alone (56.1 ± 0.736 mM and 33.1 ± 0.920 mM, respectively). To our knowledge, this is the first report of 3-HP production by E. coli harboring the Pdu pathway, with the dual synthetic pathway showing the highest yield ever reported by batch culture [54.1% (mol/mol)].

Microbial production of short chain diols

Short chain diols (propanediols, butanediols, pentanediols) have been widely used in bulk and fine chemical industries as fuels, solvents, polymer monomers and pharmaceutical precursors. The chemical production of short chain diols from fossil resources has been developed and optimized for decades. Consideration of the exhausting fossil resources and the increasing environment issues, the bio-based process to produce short chain diols is attracting interests. Currently, a variety of biotechnologies have been developed for the microbial production of the short chain diols from renewable feed-stocks. In order to efficiently produce bio-diols, the techniques like metabolically engineering the production strains, optimization of the fermentation processes, and integration of a reasonable downstream recovery processes have been thoroughly investigated. In this review, we summarized the recent development in the whole process of bio-diols production including substrate, microorganism, metabolic pathway, fermentation process and downstream process.

Coenzyme B12 can be produced by engineered Escherichia coli under both anaerobic and aerobic conditions

Coenzyme B12 (Vitamin B12 ) is one of the most complex biomolecules and an essential cofactor required for the catalytic activity of many enzymes. Pseudomonas denitrificans synthesizes coenzyme B12 in an oxygen-dependent manner using a pathway encoded by more than 25 genes that are located in six different operons. Escherichia coli, a robust and suitable host for metabolic engineering was used to produce coenzyme B12 . These genes were cloned into three compatible plasmids and expressed heterologously in E. coli BL21 (DE3). Real-time PCR, SDS-PAGE analysis and bioassay showed that the recombinant E. coli expressed the coenzyme B12 synthetic genes and successfully produced coenzyme B12 . However, according to the quantitative determination by inductively coupled plasma-mass spectrometry, the amount of coenzyme B12 produced by the recombinant E. coli (0.21 ± 0.02 μg/g cdw) was approximately 13-fold lower than that by P. denitrificans (2.75 ± 0.22 μg/g cdw). Optimization of the culture conditions to improve the production of coenzyme B12 by the recombinant E. coli was successful, and the highest titer (0.65 ± 0.03 μg/g cdw) of coenzyme B12 was obtained. Interestingly, although the synthesis of coenzyme B12 in P. denitrificans is strictly oxygen-dependent, the recombinant E. coli could produce coenzyme B12 under anaerobic conditions.