Recent advances in the metabolic engineering of microorganisms for the production of 3-hydroxypropionic acid as C3 platform chemical

Engineering oleaginous red yeasts as versatile chassis for the production of oleochemicals and valuable compounds: Current advances and perspectives

Enabling the transition towards a future circular bioeconomy based on industrial biomanufacturing necessitates the development of efficient and versatile microbial platforms for sustainable chemical and fuel production. Recently, there has been growing interest in engineering non-model microbes as superior biomanufacturing platforms due to their broad substrate range and high resistance to stress conditions. Among these non-conventional microbes, red yeasts belonging to the genus Rhodotorula have emerged as promising industrial chassis for the production of specialty chemicals such as oleochemicals, organic acids, fatty acid derivatives, terpenoids, and other valuable compounds. Advancements in genetic and metabolic engineering techniques, coupled with systems biology analysis, have significantly enhanced the production capacity of red yeasts. These developments have also expanded the range of substrates and products that can be utilized or synthesized by these yeast species. This review comprehensively examines the current efforts and recent progress made in red yeast research. It encompasses the exploration of available substrates, systems analysis using multi-omics data, establishment of genome-scale models, development of efficient molecular tools, identification of genetic elements, and engineering approaches for the production of various industrially relevant bioproducts. Furthermore, strategies to improve substrate conversion and product formation both with systematic and synthetic biology approaches are discussed, along with future directions and perspectives in improving red yeasts as more versatile biotechnological chassis in contributing to a circular bioeconomy. The review aims to provide insights and directions for further research in this rapidly evolving field. Ultimately, harnessing the capabilities of red yeasts will play a crucial role in paving the way towards next-generation sustainable bioeconomy.

Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis

Our previous study's introduction of the malonic acid assimilation pathway into Escherichia coli enabled biosynthesis of 3-Hydroxypropionate (3-HP) from malonate. However, the relatively low uptake activity of tripartite ATP-independent periplasmic (TRAP) malonic acid transporter (MatPQM) is considered rate-limiting in malonate utilization. Here, to improve the transport performance of this importer, MatP variants were obtained via directed evolution and a novel developed enzyme-inhibition-based high throughput screening approach. This plate chromogenic screening method is based on the fact that malonic acid inhibits both of succinate dehydrogenase activity and further the capability of the reduction of methylene-blue to methylene-white. The best mutant E103G/S194G/Y218H/L235P/N272S showed twofold increased transport efficiency compared to the wild-type. ITC assay and structural analysis revealed that increased binding affinity of the mutant to the ligand was the reason for improved uptake activity of MatPQM. Finally, the engineered strain harboring the evolved mutant produced 20.08 g/L 3-HP with the yield of 0.87 mol/mol malonate in a bioreactor. Therefore, the well-established directed evolution strategy can be regarded as the reference work for other TRAP-type transporters engineering. And, this transporter mutant with enhanced malonic acid uptake activity has broad applications in the microbial biosynthesis of malonyl-CoA-derived valuable compounds in bacteria. KEY POINTS: • We reported directed evolution of a TRAP-type malonic acid transporter. • We found the enhanced malonate uptake activity of mutant lies in improved affinity. • We enhanced 3-HP bioproduction with high yield by employing the best mutant.

Biocatalytic synthesis of 2-fluoro-3-hydroxypropionic acid

Fluorine has become an important element for the design of synthetic molecules for use in medicine, agriculture, and materials. The introduction of fluorine atoms into organic compound molecules can often give these compounds new functions and make them have better performance. Despite the many advantages provided by fluorine for tuning key molecular properties, it is rarely found in natural metabolism. We seek to expand the molecular space available for discovery through the development of new biosynthetic strategies that cross synthetic with natural compounds. Towards this goal, 2-fluoro-3-hydroxypropionic acid (2-F-3-HP) was first synthesized using E. coli coexpressing methylmalonyl CoA synthase (MatBrp), methylmalonyl CoA reductase (MCR) and malonate transmembrane protein (MadLM). The concentration of 2-F-3-HP reached 50.0 mg/L by whole-cell transformation after 24 h. 2-F-3-HP can be used as the substrate to synthesize other fluorides, such as poly (2-fluoro-3-hydroxypropionic acid) (FP3HP). Being entirely biocatalytic, our procedure provides considerable advantages in terms of environmental and safety impacts over reported chemical methods.

Structure Based Protein Engineering of Aldehyde Dehydrogenase from Azospirillum brasilense to Enhance Enzyme Activity against Unnatural 3-Hydroxypropionaldehyde

3-Hydroxypropionic acid (3HP) is a platform chemical and can be converted into other valuable C3-based chemicals. Because a large amount of glycerol is produced as a by-product in the biodiesel industry, glycerol is an attractive carbon source in the biological production of 3HP. Although eight 3HP-producing aldehyde dehydrogenases (ALDHs) have been reported so far, the low conversion rate from 3-hydroxypropionaldehyde (3HPA) to 3HP using these enzymes is still a bottleneck for the production of 3HP. In this study, we elucidated the substrate binding modes of the eight 3HP-producing ALDHs through bioinformatic and structural analysis of these enzymes and selected protein engineering targets for developing enzymes with enhanced enzymatic activity against 3HPA. Among ten AbKGSADH variants we tested, three variants with replacement at the Arg281 site of AbKGSADH showed enhanced enzymatic activities. In particular, the AbKGSADH^R281Y variant exhibited improved catalytic efficiency by 2.5-fold compared with the wild type.

Coupled synthetic pathways improve the production of 3-hydroxypropionic acid in recombinant Escherichia coli strains

To improve the production of 3-HP with glucose as a substrate, the malonyl-CoA and propionyl-CoA pathways were coupled to regulate NADP+/NADPH regeneration in the recombinant E. coli. The strain Ec-AM that overexpressed the key enzymes of the malonyl-CoA pathway, acetyl CoA carboxylase (ACC) from Ustilago maydis and malonyl CoA reductase (MCR) from Chloroflexus aurantiacus, produced 0.26 g/L of 3-HP in 25-h shake flask cultivation. The strain Ec-P overexpressing the key enzyme of the propionyl-CoA pathway, propionyl-CoA dehydrogenase (PACD) from Candida rugosa, produced 0.11 g/L of 3-HP. However, 3-HP titer of the strain Ec-PAM overexpressing PACD along with ACC and MCR, via two pathways cooperation, was 1.29 g/L. The addition of biotin and bicarbonate improved the 3-HP production of the strain Ec-PAM. 3-HP titer of strain Ec-ΔY-ΔP-PAM with double deletion of ygfH (encoding propionyl-CoA: succinate-CoA transferase) and prpC (encoding methylcitrate synthase) genes reached 1.94 g/L, which was 1.5-fold higher than that of the strain Ec-PAM cultured under the same conditions.

Development of Pseudomonas asiatica as a host for the production of 3-hydroxypropionic acid from glycerol

Pseudomonas asiatica C1, which could grow on glucose and aerobically synthesize coenzyme B₁₂, was isolated and developed as a microbial cell factory for the production of 3-hydroxypropionic acid (3-HP) from glycerol. Three heterologous enzymes, glycerol dehydratase (GDHt), GDHt reactivase (GdrAB) and aldehyde dehydrogenase (ALDH), constituting the 3-HP synthesis pathway, were introduced, and three putative dehydrogenases, responsible for 3-HP degradation, were disrupted. In addition, the transcriptional repressor glpR and the glycerol kinase glpK were removed to increase glycerol import while eliminating the catabolic use of glycerol. Furthermore, the global regulatory protein encoded by crc and several putative oxidoreductases (PDORs) were disrupted. One resulting strain, when grown on glucose, could produce 3-HP at ~ 700 mM in 48 h in a fed-batch bioreactor experiment, with the molar yield > 0.99 on glycerol without much by-products. This study demonstrates that P. asiatica C1 is a promising host for production of 3-HP from glycerol.

Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4 × after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Type II methanotrophs: A promising microbial cell-factory platform for bioconversion of methane to chemicals

Methane, the predominant element in natural gas and biogas, represents a promising alternative to carbon feedstocks in the biotechnological industry due to its low cost and high abundance. The bioconversion of methane to value-added products can enhance the value of gas and mitigate greenhouse gas emissions. Methanotrophs, methane-utilizing bacteria, can make a significant contribution to the production of various valuable biofuels and chemicals from methane. Type II methanotrophs in comparison with Type I methanotrophs have distinct advantages, including high acetyl-CoA flux and the co-incorporation of two important greenhouse gases (methane and CO₂), making it a potential microbial cell-factory platform for methane-derived biomanufacturing. Herein, we review the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. Representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.

Recent Progress in the Understanding and Engineering of Coenzyme B12-Dependent Glycerol Dehydratase

Coenzyme B₁₂-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B₁₂-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.

High-level production of 3-hydroxypropionic acid from glycerol as a sole carbon source using metabolically engineered Escherichia coli

As climate change is an important environmental issue, the conventional petrochemical-based processes to produce valuable chemicals are being shifted toward eco-friendly biological-based processes. In this study, 3-hydroxypropionic acid (3-HP), an industrially important three carbon (C3) chemical, was overproduced by metabolically engineered Escherichia coli using glycerol as a sole carbon source. As the first step to construct a glycerol-dependent 3-HP biosynthetic pathway, the dhaB1234 and gdrAB genes from Klebsiella pneumoniae encoding glycerol dehydratase and glycerol reactivase, respectively, were introduced into E. coli to convert glycerol into 3-hydroxypropionaldehyde (3-HPA). In addition, the ydcW gene from K. pneumoniae encoding γ-aminobutyraldehyde dehydrogenase, among five aldehyde dehydrogenases examined, was selected to further convert 3-HPA to 3-HP. Increasing the expression level of the ydcW gene enhanced 3-HP production titer and reduced 1,3-propanediol production. To enhance 3-HP production, fed-batch fermentation conditions were optimized by controlling dissolved oxygen (DO) level and employing different feeding strategies including intermittent feeding, pH-stat feeding, and continuous feeding strategies. Fed-batch culture of the final engineered E. coli strain with DO control and continuous feeding strategy produced 76.2 g/L of 3-HP with the yield and productivity of 0.457 g/g glycerol and 1.89 g·L^-1 ·h^-1 , respectively. To the best of our knowledge, this is the highest 3-HP productivity achieved by any microorganism reported to date.

A Review of the Biotechnological Production of Methacrylic Acid

Industrial biotechnology can lead to new routes and potentially to more sustainable production of numerous chemicals. We review the potential of biobased routes from sugars to the large volume commodity, methacrylic acid, involving fermentation based bioprocesses. We cover the key progress over the past decade on direct and indirect fermentation based routes to methacrylic acid including both academic as well as patent literature. Finally, we take a critical look at the potential of biobased routes to methacrylic acid in comparison with both incumbent as well as newer greener petrochemical based processes.

Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway

We engineered a type II methanotroph, Methylosinus trichosporium OB3b, for 3-hydroxypropionic acid (3HP) production by reconstructing malonyl-CoA pathway through heterologous expression of Chloroflexus aurantiacus malonyl-CoA reductase (MCR), a bifunctional enzyme. Two strategies were designed and implemented to increase the malonyl-CoA pool and thus, increase in 3HP production. First, we engineered the supply of malonyl-CoA precursors by overexpressing endogenous acetyl-CoA carboxylase (ACC), substantially enhancing the production of 3HP. Overexpression of biotin protein ligase (BPL) and malic enzyme (NADP⁺-ME) led to a ∼22.7% and ∼34.5% increase, respectively, in 3HP titer in ACC-overexpressing cells. Also, the acetyl-CoA carboxylation bypass route was reconstructed to improve 3HP productivity. Co-expression of methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii and phosphoenolpyruvate carboxylase (PEPC), which provides the MMC precursor, further improved the 3HP titer. The highest 3HP production of 49 mg/L in the OB3b-MCRMP strain overexpressing MCR, MMC and PEPC resulted in a 2.4-fold improvement of titer compared with that in the only MCR-overexpressing strain. Finally, we could obtain 60.59 mg/L of 3HP in 42 h using the OB3b-MCRMP strain through bioreactor operation, with a 6.36-fold increase of volumetric productivity compared than that in the flask cultures. This work demonstrates metabolic engineering of type II methanotrophs, opening the door for using type II methanotrophs as cell factories for biochemical production along with mitigation of greenhouse gases.

Engineering Corynebacterium glutamicum for the Efficient Production of 3-Hydroxypropionic Acid from a Mixture of Glucose and Acetate via the Malonyl-CoA Pathway

3-Hydroxypropionic acid (3-HP) has been recognized as one of the top value-added building block chemicals, due to its numerous potential applications. Over the past decade, biosynthesis of 3-HP via the malonyl-CoA pathway has been increasingly favored because it is balanced in terms of ATP and reducing equivalents, does not require the addition of costly coenzymes, and can utilize renewable lignocellulosic biomass. In this study, gene mcr encoding malonyl-CoA reductase from Chloroflexus aurantiacus was introduced into Corynebacterium glutamicum ATCC13032 to construct the strain Cgz1, which accumulated 0.30 g/L 3-HP. Gene ldhA encoding lactate dehydrogenase was subsequently deleted to eliminate lactate accumulation, but this decreased 3-HP production and greatly increased acetate accumulation. Then, different acetate utilization genes were overexpressed to reuse the acetate, and the best candidate Cgz5 expressing endogenous gene pta could effectively reduce the acetate accumulation and produced 0.68 g/L 3-HP. To enhance the supply of the precursor acetyl-CoA, acetate was used as an ancillary carbon source to improve the 3-HP production, and 1.33 g/L 3-HP could be produced from a mixture of glucose and acetate, with a 2.06-fold higher yield than from glucose alone. Finally, to inhibit the major 3-HP competing pathway-fatty acid synthesis, 10 μM cerulenin was added and strain Cgz5 produced 3.77 g/L 3-HP from 15.47 g/L glucose and 4.68 g/L acetate with a yield of 187 mg/g substrate in 48 h, which was 12.57-fold higher than that of Cgz1. To our best knowledge, this is the first report on engineering C. glutamicum to produce 3-HP via the malonyl-CoA pathway. The results indicate that the innocuous biosafety level I microorganism C. glutamicum is a potential industrial 3-HP producer.

Structural insight into bi-functional malonyl-CoA reductase

The bi-functional malonyl-CoA reductase is a key enzyme of the 3-hydroxypropionate bi-cycle for bacterial CO₂ fixation, catalysing the reduction of malonyl-CoA to malonate semialdehyde and further reduction to 3-hydroxypropionate. Here, we report the crystal structure and the full-length architecture of malonyl-CoA reductase from Porphyrobacter dokdonensis. The malonyl-CoA reductase monomer of 1230 amino acids consists of four tandemly arranged short-chain dehydrogenases/reductases, with two catalytic and two non-catalytic short-chain dehydrogenases/reductases, and forms a homodimer through paring contact of two malonyl-CoA reductase monomers. The complex structures with its cofactors and substrates revealed that the malonyl-CoA substrate site is formed by the cooperation of two short-chain dehydrogenases/reductases and one novel extra domain, while only one catalytic short-chain dehydrogenase/reductase contributes to the formation of the malonic semialdehyde-binding site. The phylogenetic and structural analyses also suggest that the bacterial bi-functional malonyl-CoA has a structural origin that is completely different from the archaeal mono-functional malonyl-CoA and malonic semialdehyde reductase, and thereby constitute an efficient enzyme.

Efficient Synthesis of Methyl 3-Acetoxypropionate by a Newly Identified Baeyer-Villiger Monooxygenase

Baeyer-Villiger monooxygenases (BVMOs) are an emerging class of promising biocatalysts for the oxidation of ketones to prepare corresponding esters or lactones. Although many BVMOs have been reported, the development of highly efficient enzymes for use in industrial applications is desirable. In this work, we identified a BVMO from Rhodococcus pyridinivorans (BVMO_Rp) with a high affinity toward aliphatic methyl ketones (K_m < 3.0 μM). The enzyme was highly soluble and relatively stable, with a half-life of 23 h at 30°C and pH 7.5. The most effective substrate discovered so far is 2-hexanone (k _cat = 2.1 s^-1; K_m = 1.5 μM). Furthermore, BVMO_Rp exhibited excellent regioselectivity toward most aliphatic ketones, preferentially forming typical (i.e., normal) products. Using the newly identified BVMO_Rp as the catalyst, a high concentration (26.0 g/liter; 200 mM) of methyl levulinate was completely converted to methyl 3-acetoxypropionate after 4 h, with a space-time yield of 5.4 g liter^-1 h^-1 Thus, BVMO_Rp is a promising biocatalyst for the synthesis of 3-hydroxypropionate from readily available biobased levulinate to replace the conventional fermentation.IMPORTANCE BVMOs are emerging as a green alternative to traditional oxidants in the BV oxidation of ketones. Although many BVMOs are discovered and used in organic synthesis, few are really applied in industry, especially in the case of aliphatic ketones. Herein, a highly soluble and relatively stable monooxygenase from Rhodococcus pyridinivorans (BVMO_Rp) was identified with high activity and excellent regioselectivity toward most aliphatic ketones. BVMO_Rp possesses unusually high substrate loading during the catalysis of the oxidation of biobased methyl levulinate to 3-hydroxypropionic acid derivatives. This study indicates that the synthesis of 3-hydroxypropionate from readily available biobased levulinate by BVMO_Rp-catalyzed oxidation holds great promise to replace traditional fermentation.

Screening, expression, purification and characterization of CoA-transferases for lactoyl-CoA generation

Lactoyl-CoA is critical for the biosynthesis of biodegradable and biocompatible lactate-based copolymers, which have wide applications. However, reports on acetyl-CoA: lactate CoA-transferases (ALCTs) are rare. To exploit novel ALCTs, amino acid sequence similarity searches based on the CoA-transferases from Clostridium propionicum and Megasphaera elsdenii were conducted. Two known and three novel enzymes were expressed, purified and characterized. Three novel ALCTs were identified, one each from Megasphaera sp. DISK 18, Clostridium lactatifermentans An75 and Firmicutes bacterium CAG: 466. ME-PCT from Megasphaera elsdenii had the highest catalytic efficiency for both acetyl-CoA (264.22 s^-1 mM^-1) and D-lactate (84.18 s^-1 mM^-1) with a broad temperature range for activity and good stability. This study, therefore, offers novel and efficient enzymes for lactoyl-CoA generation. To our best knowledge, this is the first report on the systematic mining of ALCTs, which offers valuable new tools for the engineering of pathways that rely on these enzymes.

The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16

BACKGROUND

3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO₂ and H₂.

RESULTS

When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism's ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co-metabolise 3-HP alongside other carbon and energy sources such as fructose and CO₂/H₂. Further analysis suggested primary roles for the different mmsA operons in the utilisation of β-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3).

CONCLUSIONS

Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.

Metabolic Engineering of Yeast for the Production of 3-Hydroxypropionic Acid

The beta-hydroxy acid 3-hydroxypropionic acid (3-HP) is an attractive platform compound that can be used as a precursor for many commercially interesting compounds. In order to reduce the dependence on petroleum and follow sustainable development, 3-HP has been produced biologically from glucose or glycerol. It is reported that 3-HP synthesis pathways can be constructed in microbes such as Escherichia coli, Klebsiella pneumoniae and the yeast Saccharomyces cerevisiae. Among these host strains, yeast is prominent because of its strong acid tolerance which can simplify the fermentation process. Currently, the malonyl-CoA reductase pathway and the β-alanine pathway have been successfully constructed in yeast. This review presents the current developments in 3-HP production using yeast as an industrial host. By combining genome-scale engineering tools, malonyl-CoA biosensors and optimization of downstream fermentation, the production of 3-HP in yeast has the potential to reach or even exceed the yield of chemical production in the future.

Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD+, for enhancing the production of 3-hydroxypropionic acid

3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD⁺ regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues. The residues in the binding sites for the substrates, 3-HPA and NAD⁺, were randomized, and the resulting libraries were screened for higher activity. Isolated KGSADH variants had significantly lower K_m values for both the substrates. The enzymes also showed higher substrate specificities for aldehyde and NAD⁺, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain with one of the engineered KGSADH variants exhibited less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that with the wild-type KGSADH. The flask culture of the P. denitrificans strain with the mutant KGSADH resulted in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM).

Production of 3-hydroxypropionic acid via the malonyl-CoA pathway using recombinant fission yeast strains

3-Hydroxypropionic acid (3-HP) can be converted into derivatives such as acrylic acid, a source for producing super absorbent polymers. Although Escherichia coli has often been used for 3-HP production, it exhibits low tolerance to 3-HP. To circumvent this problem, we selected the fission yeast Schizosaccharomyces pombe as this microorganism has higher tolerance to 3-HP than E. coli. Therefore, we constructed S. pombe transformants overexpressing two genes, one encoding the S. pombe acetyl-CoA carboxylase (Cut6p) and the other encoding the malonyl-CoA reductase derived from Chloroflexus aurantiacus (CaMCR). To prevent the degradation of these expressed proteins, we employed an S. pombe protease-deficient strain. Moreover, to increase the cytosolic concentration of acetyl-CoA, we supplemented acetate to the medium, which improved 3-HP production. To further produce 3-HP by overexpressing Cut6p and CaMCR, we exploited the highly expressing S. pombe hsp9 promoter. Finally, culturing in high-density reached 3-HP production to 7.6 g/L at 31 h.

Characterisation of a 3-hydroxypropionic acid-inducible system from Pseudomonas putida for orthogonal gene expression control in Escherichia coli and Cupriavidus necator

3-hydroxypropionic acid (3-HP) is an important platform chemical used as a precursor for production of added-value compounds such as acrylic acid. Metabolically engineered yeast, Escherichia coli, cyanobacteria and other microorganisms have been developed for the biosynthesis of 3-HP. Attempts to overproduce this compound in recombinant Pseudomonas denitrificans revealed that 3-HP is consumed by this microorganism using the catabolic enzymes encoded by genes hpdH, hbdH and mmsA. 3-HP-inducible systems controlling the expression of these genes have been predicted in proteobacteria and actinobacteria. In this study, we identify and characterise 3-HP-inducible promoters and their corresponding LysR-type transcriptional regulators from Pseudomonas putida KT2440. A newly-developed modular reporter system proved possible to demonstrate that PpMmsR/P_mmsA and PpHpdR/P_hpdH are orthogonal and highly inducible by 3-HP in E. coli (12.3- and 23.3-fold, respectively) and Cupriavidus necator (51.5- and 516.6-fold, respectively). Bioinformatics and mutagenesis analyses revealed a conserved 40-nucleotide sequence in the hpdH promoter, which plays a key role in HpdR-mediated transcription activation. We investigate the kinetics and dynamics of the PpHpdR/P_hpdH switchable system in response to 3-HP and show that it is also induced by both enantiomers of 3-hydroxybutyrate. These findings pave the way for use of the 3-HP-inducible system in synthetic biology and biotechnology applications.

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis

3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP.

Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense

3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD⁺. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.

Engineering Plasmid-Free Klebsiella Pneumoniae for Production of 3-Hydroxypropionic Acid

Although plasmid-dependent microbial breeding is predominant in manufacturing bio-based chemicals, it shows pitfall of genetic instability and thus hinders industrial production. Alternatively, chromosome engineering free from plasmid enables genetic stability and thus represents the new trend of microbial breeding. 3-Hydroxypropionic acid (3-HP) is an economically important platform compound as the versatile precursor of a suite of C3 compound, such as 1, 3-PDO. Klebsiella pneumoniae is regarded as a promising host strain due to both its dha regulon and exceptional glycerol fermentation ability. To produce 3-HP in K. pneumoniae, the IS1 region in chromosome was replaced with the AD DNA cassette containing aldH gene from E.coli through homologous recombination approach. The engineered recombinant converted glycerol into 3-HPA and then 3-HP when 40 g/L of initial glycerol was added. The novelties of this study comprise (i) the genetic stability of plasmid-free strains (ii) without using any inducer and antibiotics and thus more applicable than plasmid-based strains.

Engineering Biosynthesis Mechanisms for Diversifying Polyhydroxyalkanoates

Polyhydroxyalkanoates (PHA) are a family of diverse biopolyesters synthesized by bacteria. PHA diversity, as reflected by its monomers, homopolymers, random and block copolymers, as well as functional polymers, can now be generated by engineering the three basic synthesis pathways including the acetoacetyl-CoA pathway, in situ fatty acid synthesis, and/or β-oxidation cycles, as well as PHA synthase specificity. It is now possible to tailor the PHA structures via genome editing or process engineering. The increasing PHA diversity and maturing PHA production technology should lead to more focused research into their low-cost and/or high-value applications.

Enzymatic Synthesis of Biobased Polyesters and Polyamides

Nowadays, "green" is a hot topic almost everywhere, from retailers to universities to industries; and achieving a green status has become a universal aim. However, polymers are commonly considered not to be "green", being associated with massive energy consumption and severe pollution problems (for example, the "Plastic Soup") as a public stereotype. To achieve green polymers, three elements should be entailed: (1) green raw materials, catalysts and solvents; (2) eco-friendly synthesis processes; and (3) sustainable polymers with a low carbon footprint, for example, (bio)degradable polymers or polymers which can be recycled or disposed with a gentle environmental impact. By utilizing biobased monomers in enzymatic polymerizations, many advantageous green aspects can be fulfilled. For example, biobased monomers and enzyme catalysts are renewable materials that are derived from biomass feedstocks; enzymatic polymerizations are clean and energy saving processes; and no toxic residuals contaminate the final products. Therefore, synthesis of renewable polymers via enzymatic polymerizations of biobased monomers provides an opportunity for achieving green polymers and a future sustainable polymer industry, which will eventually play an essential role for realizing and maintaining a biobased and sustainable society.

Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae

The establishment of a heterologous pathway in a microbial host for the production of industrially relevant chemicals at high titers and yields requires efficient adjustment of the central carbon metabolism to ensure that flux is directed toward the product of interest. This can be achieved through regulation at key branch points in the metabolic networks, and here we present a novel approach for dynamic modulation of pathway flux and enzyme expression levels. The approach is based on a hierarchical dynamic control system around the key pathway intermediate malonyl-CoA. The upper level of the control system ensures downregulation of endogenous use of malonyl-CoA for fatty acid biosynthesis, which results in accumulation of this pathway intermediate. The lower level of the control system is based on use of a novel biosensor for malonyl-CoA to activate expression of a heterologous pathway using this metabolite for production of 3-hydroxypropionic acid (3-HP). The malonyl-CoA sensor was developed based on the FapR transcription factor of Bacillus subtilis, and it demonstrates one of the first applications of a bacterial metabolite sensor in yeast. Introduction of the dual pathway control increased the production of 3-HP by 10-fold and can also be applied for production of other malonyl-CoA-derived products.

Genetically encoded sensors enable real-time observation of metabolite production

Engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allows us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of $14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of $51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.

Toward glycerol biorefinery: metabolic engineering for the production of biofuels and chemicals from glycerol

As an inevitable by-product of the biofuel industry, glycerol is becoming an attractive feedstock for biorefinery due to its abundance, low price and high degree of reduction. Converting crude glycerol into value-added products is important to increase the economic viability of the biofuel industry. Metabolic engineering of industrial strains to improve its performance and to enlarge the product spectrum of glycerol biotransformation process is highly important toward glycerol biorefinery. This review focuses on recent metabolic engineering efforts as well as challenges involved in the utilization of glycerol as feedstock for the production of fuels and chemicals, especially for the production of diols, organic acids and biofuels.

Biobased organic acids production by metabolically engineered microorganisms

Bio-based production of organic acids via microbial fermentation has been traditionally used in food industry. With the recent desire to develop more sustainable bioprocesses for production of fuels, chemicals and materials, the market for microbial production of organic acids has been further expanded as organic acids constitute a key group among top building block chemicals that can be produced from renewable resources. Here we review the current status for production of citric acid and lactic acid, and we highlight the use of modern metabolic engineering technologies to develop high performance microbes for production of succinic acid and 3-hydroxypropionic acid. Also, the key limitations and challenges in microbial organic acids production are discussed.

Enhancement of 3-hydroxypropionic acid production from glycerol by using a metabolic toggle switch

Background

3-hydroxypropionic acid (3-HP) is an important platform for the production of C3 chemicals, including acrylic acid, methyl acrylate, and acrylamide. Microbial production of 3-HP is mainly due to glycerol metabolism. In this study, in order to improve microbial 3-HP production, we applied a metabolic toggle switch for controlling the glycerol metabolism to redirect the excess metabolic flux of central metabolic pathway toward an exogenous 3-HP producing pathway in Escherichia coli.

Results

The metabolic toggle switch enables conditional repression of the expression of a target gene during the fermentation. We individually performed conditional repression of glpK, tpiA, and gapA, which are involved in glycerol metabolism. The conditional repression of glpK and tpiA was not effective for 3-HP production under our experimental conditions. However, gapA conditional repression contributed to improve 3-HP production (titer, 54.2 ± 1.5 mM; yield, 32.1 ± 1.3 %) compared with that for the wild type strain. Additional deletion of endogenous yqhD, which is responsible for the production of a major byproduct, 1,3-propandiol, further increased 3-HP production (titer, 67.3 ± 2.1 mM; yield, 51.5 ± 3.2 %). The titer and yield were 80 and 94 % higher than those of the wild type strain, respectively. The obtained 3-HP yield from glycerol is comparable with the highest yield ever reported for microbial 3-HP production using glycerol as a sole carbon source. The measurement of intracellular metabolites showed the metabolic toggle switch successfully controlled the metabolic flux.

Conclusion

The conditional repression of gapA by using the metabolic toggle switch combined with deletion of endogeneous yqhD increased 3-HP production approximately twofold from glycerol. This result indicates the metabolic toggle switch can be applied in various bio-production using diverse substrates.

Non-hazardous Baeyer-Villiger oxidation of levulinic acid derivatives: alternative renewable access to 3-hydroxypropionates

Baeyer-Villiger monooxygenases catalyze the energetically challenging oxidation of levulinates (4-oxopentanoates) to 3-hydroxypropionic acid (3-HPA) derivates under ambient conditions, replacing propellant-grade H2O2 with aerial oxygen as the oxidant. This reaction enables a new pathway to a platform for chemical 3-HPA, an important intermediate in the non-petrol based production of a variety of bulk chemicals (acrylates, malonates, 1,3-propanediol).

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)].

Contemplating 3-Hydroxypropionic Acid Biosynthesis in Klebsiella pneumoniae

3-Hydroxypropionic acid (3-HP) is a commercially valuable platform chemical from which an array of C3 compounds can be generated. Klebsiella pneumoniae has been considered a promising species for biological production of 3-HP. Despite a wealth of reports related to 3-HP biosynthesis in K. pneumoniae, its commercialization is still in infancy. The major hurdle hindering 3-HP overproduction lies in the poor understanding of glycerol dissimilation in K. pneumoniae. To surmount this problem, this review aims to portray a picture of 3-HP biosynthesis, involving 3-HP-synthesizing strains, biochemical attributes, metabolic pathways and key enzymes. Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, here we advocate protocols for overproducing 3-HP in K. pneumoniae. These protocols range from cofactor regeneration, alleviation of metabolite toxicity, genome editing, remodeling of transport system, to carbon flux partition via logic gate. The feasibility for these protocols was also discussed.

Biorefineries for the production of top building block chemicals and their derivatives

Due to the growing concerns on the climate change and sustainability on petrochemical resources, DOE selected and announced the bio-based top 12 building blocks and discussed the needs for developing biorefinery technologies to replace the current petroleum based industry in 2004. Over the last 10 years after its announcement, many studies have been performed for the development of efficient technologies for the bio-based production of these chemicals and derivatives. Now, ten chemicals among these top 12 chemicals, excluding the l-aspartic acid and 3-hydroxybutyrolactone, have already been commercialized or are close to commercialization. In this paper, we review the current status of biorefinery development for the production of these platform chemicals and their derivatives. In addition, current technological advances on industrial strain development for the production of platform chemicals using micro-organisms will be covered in detail with case studies on succinic acid and 3-hydroxypropionic acid as examples.

3-Hydroxypropionaldehyde (3-HPA) quantification by HPLC using a synthetic acrolein-free 3-hydroxypropionaldehyde system as analytical standard

HPLC-based quantification of 3-HPA using a synthetic acrolein-free 3-HPA standard obtained from commercially available 1,2,4-butanetriol through a straightforward and easy synthetic process.

Construction of Escherichia Coli Cell Factories for Production of Organic Acids and Alcohols

Production of bulk chemicals from renewable biomass has been proved to be sustainable and environmentally friendly. Escherichia coli is the most commonly used host strain for constructing cell factories for production of bulk chemicals since it has clear physiological and genetic characteristics, grows fast in minimal salts medium, uses a wide range of substrates, and can be genetically modified easily. With the development of metabolic engineering, systems biology, and synthetic biology, a technology platform has been established to construct E. coli cell factories for bulk chemicals production. In this chapter, we will introduce this technology platform, as well as E. coli cell factories successfully constructed for production of organic acids and alcohols.

3-Hydroxypropionaldehyde-specific aldehyde dehydrogenase from Bacillus subtilis catalyzes 3-hydroxypropionic acid production in Klebsiella pneumoniae

In Klebsiella pneumoniae, aldehyde dehydrogenases (ALDH) convert 3-hydroxypropionaldehyde (3-HPA) into 3-hydroxypropionic acid (3-HP). Although ALDHs can increase the production of 3-HP in K. pneumoniae, the substrate specificity of ALDH homologues from other microorganisms toward 3-HPA is less documented. Here we report that DhaS, a putative ALDH from Bacillus subtilis, shows high specificity toward 3-HPA when heterologously expressed in K. pneumoniae. Using NAD(+) as a cofactor, DhaS exhibited higher catalytic activity (2.3 U mg(-1)) and lower K m value (0.4 mmol l(-1)) toward 3-HPA than that toward other aldehydes. Under shake-flask conditions, the recombinant strain produced 2.1 g 3-HP l(-1) in 24 h, which is 3.9-fold of that in a control harboring a blank vector. Under non-optimized bioreactor conditions, the recombinant strain produced 18 g 3-HP l(-1) and 1,3-propanediol (1,3-PDO) at 27 g l(-1) in 24 h. The overall conversion rate from glycerol to 3-HP and 1,3-PDO reached 59.4 mol mol(-1). Homology modeling of DhaS illustrates substrate specificity and NAD(+)-binding site. DhaS is thus a 3-HPA-specific enzyme useful for production of 3-HP.

Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

Biologically produced 3-hydroxypropionic acid (3 HP) is a potential source for sustainable acrylates and can also find direct use as monomer in the production of biodegradable polymers. For industrial-scale production there is a need for robust cell factories tolerant to high concentration of 3 HP, preferably at low pH. Through adaptive laboratory evolution we selected S. cerevisiae strains with improved tolerance to 3 HP at pH 3.5. Genome sequencing followed by functional analysis identified the causal mutation in SFA1 gene encoding S-(hydroxymethyl)glutathione dehydrogenase. Based on our findings, we propose that 3 HP toxicity is mediated by 3-hydroxypropionic aldehyde (reuterin) and that glutathione-dependent reactions are used for reuterin detoxification. The identified molecular response to 3 HP and reuterin may well be a general mechanism for handling resistance to organic acid and aldehydes by living cells.

Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli

Background

3-hydroxypropionic acid (3HP) is an important chemical precursor for the production of bioplastics. Microbial production of 3HP from glycerol has previously been developed through the optimization of culture conditions and the 3HP biosynthesis pathway. In this study, a novel strategy for improving 3HP production in Escherichia coli was investigated by the modification of central metabolism based on a genome-scale metabolic model and experimental validation.

Results

Metabolic simulation identified the double knockout of tpiA and zwf as a candidate for improving 3HP production. A 3HP-producing strain was constructed by the expression of glycerol dehydratase and aldehyde dehydrogenase. The double knockout of tpiA and zwf increased the percentage carbon-molar yield (C-mol%) of 3HP on consumed glycerol 4.4-fold (20.1 ± 9.2 C-mol%), compared to the parental strain. Increased extracellular methylglyoxal concentrations in the ΔtpiA Δzwf strain indicated that glycerol catabolism was occurring through the methylglyoxal pathway, which converts dihydroxyacetone phosphate to pyruvate, as predicted by the metabolic model. Since the ΔtpiA Δzwf strain produced abundant 1,3-propanediol as a major byproduct (37.7 ± 13.2 C-mol%), yqhD, which encodes an enzyme involved in the production of 1,3-propanediol, was disrupted in the ΔtpiA Δzwf strain. The 3HP yield of the ΔtpiA Δzwf ΔyqhD strain (33.9 ± 1.2 C-mol%) was increased 1.7-fold further compared to the ΔtpiA Δzwf strain and by 7.4-fold compared to the parental strain.

Conclusion

This study successfully increased 3HP production by 7.4-fold in the ΔtpiA Δzwf ΔyqhD E. coli strain by the modification of the central metabolism, based on metabolic simulation and experimental validation of engineered strains.

Enhanced production of 3-hydroxypropionic acid from glycerol by modulation of glycerol metabolism in recombinant Escherichia coli

3-Hydroxypropionic acid (3-HP) is a valuable biochemical with high potential for bioplastic manufacturing. The endogenous glycerol metabolism and by-product formation pathway in Escherichia coli were modulated to enhance 3-HP production from glycerol. Double deletion of glpK and yqhD directed the glycerol flux to 3-HP biosynthesis and reduced the formation of 1,3-propanediol. Since 3-hydroxypropionaldehyde (3-HPA), a precursor of 3-HP, is toxic to cell growth, the gene encoding Pseudomonas aeruginosa semialdehyde dehydrogenase (PSALDH) highly active on 3-HPA was expressed in E. coli. Finally, fed-batch culture of recombinant E. coli BL21star(DE3) without glpK and yqhD, and expressing Lactobacillus brevis DhaB-DhaR, and P. aeruginosa PSALDH resulted in 57.3g/L 3-HP concentration, 1.59g/L-h productivity and 0.88g/g yield. In conclusion, modulation of the glycerol metabolism in combination with enhanced activity of 3-HPA dehydrogenation improved the production of 3-HP from glycerol.